Antimicrobial Resistance in Nontyphoidal Salmonella Isolated from Human and Poultry-Related Samples in Brazil: 20-Year Meta-Analysis

Genomic Differences in Antimicrobial Resistance and Virulence Among Key Salmonella Strains of Serogroups B and D1 in Brazilian Poultry

Salmonella is a significant threat to Brazilian poultry, causing economic losses and public health risks. This study analyzed 15 Salmonella isolates along with 45 retrieved complete genomes, including serovars Gallinarum, Pullorum, Enteritidis, Typhimurium, and Heidelberg. Biochemical characterization, antimicrobial susceptibility testing, whole-genome sequencing, and comparative genomics were performed. The studied strains exhibited high levels of antimicrobial resistance, particularly to tilmicosin, penicillin/novobiocin, nalidixic acid, and streptomycin. Genomic analysis revealed diverse virulence factors and antibiotic resistance genes (ARGs), with zoonotic strains showing higher virulence compared to avian-adapted strains. Multiple plasmid types carrying ARGs were identified, highlighting the potential for horizontal gene transfer. Pangenomic and phylogenomic analyses differentiated Salmonella strains from serogroup D1 from those from serogroup B. These findings emphasize the need for comprehensive surveillance and control measures to mitigate the impact of Salmonella on both animal and human health in Brazil.

Highly resistant Salmonella Heidelberg circulating in broiler farms in southern Brazil

Salmonella Heidelberg, a serotype commonly found in Southern Brazil, is characterized by its high resistance and persistence in the poultry production. This study aimed to characterize the antimicrobial resistance of S. Heidelberg strains. In total, 100 strains isolated from poultry between 2020 and 2022 were evaluated. Phenotypic analyses were performed to determine the susceptibility of 16 antimicrobial agents and detect extended-spectrum beta-lactamase (ESBL)-producing strains. Molecular analyses were performed to detect 11 antimicrobial resistance genes (using polymerase chain reaction [PCR]) and integron class 1 genes (using real-time PCR). A total of 98% of isolates was classified as multidrug-resistant. All isolates were resistant to penicillin and lincomycin. High resistance rates (> 85%) were observed for tetracycline, doxycycline, cephalexin, amoxicillin, and ceftiofur. A significant increase (p < 0.05) in antimicrobial resistance is observed for amoxicillin, cephalexin, and ceftiofur between 2020 and 2022. No significant differences (p > 0.05) were observed in antimicrobial resistance with respect to the region of isolation, season, or company. In total, 25% of isolates were ESBL producers. Integron class 1 gene was detected in only one strain, whereas sul2 was detected in 99%, tet(A) in 66%, blaTEM in 37%, strB in 17%, cmlA in 15%, and tet(B) in 11% of the strains. Other genes were not detected or were detected in < 2% of the strains. The results showed a high overall resistance, which increased over the evaluated period. The high proportions of ESBL-producing and antimicrobial resistant strains represent a risk for highly-resistant S. Heidelberg dissemination across broiler flocks.

Antimicrobial Susceptibility Profiles of Salmonella spp. Isolates from Clinical Cases of Waterfowl in Hungary Between 2022 and 2023

The global spread of antimicrobial resistance is one of the most significant challenges of the 21st century. The waterfowl sector is an economically decisive part of the poultry industry, yet it remains under-researched, and its antibiotic usage is less monitored. Our study aimed to determine the antimicrobial susceptibility of avian pathogenic Salmonella strains, which are still prevalent in ducks and geese, against antibiotics critical for both animal and human health, and to compare these findings with human resistance data. We analyzed 71 Salmonella strains, collected by the National Reference Laboratory from samples originating from 29 settlements across Hungary between 2022 and 2023, using the minimum inhibitory concentration (MIC) method. Notably, the duck strains (n = 52) exhibited 57.7% resistance to potentiated sulfonamides, 28.8% resistance to doxycycline, and 25% resistance to cefotaxime. Among the geese strains (n = 19), 52.6% showed resistance to potentiated sulfonamides, followed by 26.3% resistance to doxycycline and amoxicillin-clavulanic acid, and 15.8% resistance to cefotaxime, ceftiofur, and ceftriaxone. When compared to human resistance data, we found significantly lower resistance levels for amoxicillin in ducks (20.0%) and geese (8.3%) in the Dél-Alföld region, compared to ampicillin resistance in human samples (45.4%), in which amoxicillin analog is an antibiotic in human medicine. Resistance to ciprofloxacin was only observed in ducks (2.0%), whereas pefloxacin resistance in human medicine was notably higher (22.3%). Overall, the results for the waterfowl sector in the Dél-Alföld region of Hungary align with the international literature in several aspects. Further investigation using next-generation sequencing to identify the genetic basis of multi-resistant strains is warranted.

Trends in antimicrobial susceptibility patterns in Salmonella from human and nonhuman sources in Sao Paulo State, Brazil, 2016-2023

Antimicrobial resistance constitutes a significant global challenge to public health and development, in which non-typhoidal Salmonella emerges as a critical concern. This study investigates the prevalence and antimicrobial resistance profiles of Salmonella isolates from both human and nonhuman sources. A total of 2,511 Salmonella isolates that had been collected from 2016 to 2023 were analyzed, of which 1,724 underwent antimicrobial susceptibility testing. The main focus lied on the 10 most prevalent serotypes, totaling 957 isolates. Serotyping showed the diverse distribution of serotypes, with Heidelberg, Typhimurium, Enteritidis, and the monophasic Salmonella Typhimurium occurring most often. Antimicrobial resistance was common since 512 strains resisted at least one drug and 319 several drugs. Notably, the Heidelberg and Mbandaka serotypes, predominantly occurring in nonhuman samples, showed multidrug resistance. Salmonella Typhi remained susceptible to antimicrobials. Resistance to nalidixic acid, tetracycline, sulfonamides, and ampicillin was prevalent, whereas all isolates remained susceptible to imipenem. A reduction in susceptibility rates for aminoglycosides was observed over the study period. Extended-spectrum β-lactamase production occurred in 4.4% of the isolates, of which Heidelberg configured the most prevalent extended-spectrum β-lactamase-positive serotype. These findings underscore the importance of surveillance and effective monitoring to control this pathogen, highlighting the necessity of prioritizing public health efforts.

Investigation of the Antimicrobial Resistance of Important Pathogens Isolated from Poultry from 2015 to 2023 in the United States

Foodborne pathogens cause around 47.8 million illnesses in the U.S. annually, with antimicrobial misuse in food production, particularly in poultry processing, contributing significantly to this public health challenge. Misuse of antimicrobials can contribute to antimicrobial resistance (AMR) and make the treatment of pathogens increasingly difficult. This emphasizes the need to investigate antimicrobial resistance in U.S. poultry. This study analyzes data from the NCBI Pathogen Isolates Browser (2015-2023) to explore the relationships between antimicrobial-resistant pathogens, AMR genes, and antimicrobials detected with resistance in pathogens isolated from chicken and turkey. Using principal component analysis and hierarchical clustering, we mapped and profiled regional and temporal patterns of antimicrobial resistance. Salmonella enterica was the most prevalent antimicrobial-resistant pathogen across both chicken and turkey, with notable outbreaks, particularly in the Northeast. Antimicrobial-resistant Campylobacter jejuni was more prevalent in chicken, particularly in California and Georgia, while Escherichia coli and Shigella were more prominent in turkey, with concentrated antimicrobial resistance in Texas for pathogen samples isolated from chicken. Resistance to tetracycline and streptomycin was widespread, with distinct regional clusters: antimicrobial resistance was concentrated in states like Minnesota for pathogens isolated from chicken, while AMR found in pathogens isolated from turkey was more evenly distributed across the Midwest. Key AMR genes, such as tet(A), mdsA, and mdsB, also followed similar patterns, peaking in 2019 and significantly declining by 2022. The observed decline in AMR cases may be linked to improved biosecurity measures and disruptions in detection due to the COVID-19 pandemic. This comprehensive study of antimicrobial resistance in U.S. poultry provides valuable insights into resistance trends, which provide useful information to inform targeted interventions and policies to mitigate AMR threats in the poultry production industry. For consumers, these findings emphasize the importance of proper food handling and cooking practices to reduce the risk of exposure to resistant pathogens. Regulatory authorities should focus on enforcing stricter antimicrobial usage policies and enhancing surveillance systems to sustain the reduction in AMR cases.

Serotype Distribution and Antimicrobial Resistance of Salmonella Isolates from Poultry Sources in China

BACKGROUND

Salmonella is an important zoonotic pathogen, of which poultry products are important reservoirs. This study analyzed the prevalence, antimicrobial resistance, and characterization of Salmonella from broiler and laying hen sources in China.

METHODS

A total of 138 (12.27%) strains of Salmonella were isolated from 1125 samples from broiler slaughterhouses (20.66%, 44/213), broiler farms (18.21%, 55/302), and laying hen farms (6.39%, 39/610). Multiplex PCR was used to identify the serotypes. Antibiotic susceptibility testing to a set of 21 antibiotics was performed and all strains were screened by PCR for 24 selected antimicrobial resistance genes (ARGs). In addition, 24 strains of Salmonella were screened out by whole-genome sequencing together with 65 released Salmonella genomes to evaluate phylogenetic characteristics, multilocus sequence typing (MLST), and plasmid carriage percentages.

RESULTS

A total of 11 different serotypes were identified, with the dominance of S. Enteritidis (43/138, 31.16%), S. Newport (30/138, 21.74%), and S. Indiana (19/138, 13.77%). The results showed that S. Enteritidis (34.34%, 34/99) and S. Newport (51.28%, 20/39) were the dominant serotypes of isolates from broilers and laying hens, respectively. The 138 isolates showed the highest resistance to sulfisoxazole (SXZ, 100%), nalidixic acid (NAL, 54.35%), tetracycline (TET, 47.83%), streptomycin (STR, 39.86%), ampicillin (AMP, 39.13%), and chloramphenicol (CHL, 30.43%), while all the strains were sensitive to both tigacycline (TIG) and colistin (COL). A total of 45.65% (63/138) of the isolates were multidrug-resistant (MDR) strains, and most of them (61/63, 96.83%) were from broiler sources. The results of PCR assays revealed that 63.77% of the isolates were carrying the quinolone resistance gene qnrD, followed by gyrB (58.70%) and the trimethoprim resistance gene dfrA12 (52.17%). Moreover, a total of thirty-four ARGs, eighty-nine virulence genes, and eight plasmid replicons were detected in the twenty-four screened Salmonella strains, among which S. Indiana was detected to carry the most ARGs and the fewest plasmid replicons and virulence genes compared to the other serotypes.

CONCLUSIONS

This study revealed a high percentage of multidrug-resistant Salmonella from poultry sources, stressing the importance of continuous monitoring of Salmonella serotypes and antimicrobial resistance in the poultry chain, and emergency strategies should be implemented to address this problem.

Prevalence and Antimicrobial Resistance of Salmonella spp. Isolated From Chilled Chicken Meat Commercialized at Retail in Federal District, Brazil

Salmonella represents one of the most common foodborne pathogens, frequently associated with the contamination of poultry products, constituting a prominent worldwide public health concern. This study determined the prevalence and antimicrobial resistance of Salmonella spp. in chilled chicken meat (115 samples) commercialized at retail in the Federal District, Brazil. Microbiological tests were performed to screen for Salmonella spp. in the chicken meat samples, and the isolated strains were confirmed by the invA gene presence (PCR technique). The strains were evaluated for antimicrobial susceptibility by the disk diffusion technique (Kirby-Bauer method) and tested for the presence of the sul2, blaCTX, and tetB antimicrobial resistance genes. The Salmonella spp. prevalence in chilled chicken meat sold at retail in the Federal District, Brazil, was 46.1% (53 of 115 chicken meat samples analyzed had invA gene-positive strains). Seventy-eight strains of Salmonella spp. isolated from the 53 contaminated samples showed higher resistance to amoxicillin/clavulanic acid (83.3%), followed by sulfonamide (64.1%) and tetracycline (46.2%); 53.8% of the isolates were multidrug-resistant (MDR). The sul2 gene that confers resistance to sulfonamide was found in 53 strains (68.0%), the blaCTX gene that confers resistance to beta-lactams was identified in 39 strains (50.0%), and the tetB gene that confers resistance to tetracycline was identified in 29 strains (37.2%). The high percentage of Salmonella contamination in chicken meat can pose a risk to consumers' health due to the possibility of causing salmonellosis. In addition, many isolates were MDR and carried antimicrobial resistance genes. Public agencies can use these results to develop effective public health policies and strategies to ensure the safety of these food products.

An Overview of Antimicrobial Resistance Profiles of Publicly Available Salmonella Genomes with Sufficient Quality and Metadata

Salmonella enterica (S. enterica) is a commensal organism or pathogen causing diseases in animals and humans, as well as widespread in the environment. Antimicrobial resistance (AMR) has increasingly affected both animal and human health and continues to raise public health concerns. A decade ago, it was estimated that the increased use of whole genome sequencing (WGS) combined with sharing of public data would drastically change and improve the surveillance and understanding of Salmonella epidemiology and AMR. This study aimed to evaluate the current usefulness of public WGS data for Salmonella surveillance and to investigate the associations between serovars, antibiotic resistance genes (ARGs), and metadata. Out of 191,306 Salmonella genomes deposited in European Nucleotide Archive and NCBI databases, 47,452 WGS with sufficient minimum metadata (country, year, and source) of S. enterica were retrieved from 116 countries and isolated between 1905 and 2020. For in silico analysis of the WGS data, KmerFinder, SISTR, and ResFinder were used for species, serovars, and AMR identification, respectively. The results showed that the five common isolation sources of S. enterica are human (29.10%), avian (22.50%), environment (11.89%), water (9.33%), and swine (6.62%). The most common ARG profiles for each class of antimicrobials are β-lactam (blaTEM-1B; 6.78%), fluoroquinolone [(parC[T57S], qnrB19); 0.87%], folate pathway antagonist (sul2; 8.35%), macrolide [mph(A); 0.39%], phenicol (floR; 5.94%), polymyxin B (mcr-1.1; 0.09%), and tetracycline [tet(A); 12.95%]. Our study reports the first overview of ARG profiles in publicly available Salmonella genomes from online databases. All data sets from this study can be searched at Microreact.

Review: Current challenges in poultry nutrition, health, and welfare

The poultry industry has benefited greatly from advances in genetics, nutrition, housing and management strategies. Geneticists have made welfare and health traits important components of selection programs, and in general, modern, high-producing poultry are healthier than 30 years ago. However, increased productivity means that the birds are closer to their physiological limits, and nutrition, environment and management have become increasingly important. The move away from in-feed antibiotic growth promotors has resulted in challenges in maintaining gut health and consequently, bird performance. However, as the industry adapts to production without the use of antibiotic growth promotors, long-term benefits may be realized due to a reduction in antimicrobial resistance. Intensive selection for meat yield and efficiency are associated with an increased risk of muscle myopathies that affect bird health and meat quality. As genetic selection increased broiler production traits, it became necessary to restrict parent stock nutrient intake in order to prevent excessive muscle and fat deposition, reduce metabolic disease, and maintain ovarian control. With continued selection for broiler production traits, the degree of restriction implemented has become a welfare issue. Additionally, recent research suggests that highly efficient broiler lines may have limited fat deposition and therefore energy reserves to support sexual maturation and egg production, especially if typical broiler breeder BW targets are maintained. A re-examination of broiler breeder feeding programs is necessary to maintain productivity and welfare. Modern laying hens are capable of laying cycles in excess of 100 weeks of age. This has reduced the use of stress-inducing forced molting programs and reduces the total number of hens needed to meet the demand for egg production. The important role of the skeletal system in eggshell deposition demands that skeletal development during rearing be carefully managed to avoid shell and skeletal problems at the end of the production cycle. As the production potential of modern poultry continues to increase through genetic and genomic selection, even greater care must be paid in order to maintain bird health and welfare. The poultry industry has successfully faced many challenges in the past and is likely to overcome the existing challenges as well.

Antimicrobial resistance and genetic background of non-typhoidal Salmonella enterica strains isolated from human infections in São Paulo, Brazil (2000-2019)

Salmonella enterica causes Salmonellosis, an important infection in humans and other animals. The number of multidrug-resistant (MDR) phenotypes associated with Salmonella spp. isolates is increasing worldwide, causing public health concern. Here, we aim to characterize the antimicrobial-resistant phenotype of 789 non-typhoidal S. enterica strains isolated from human infections in the state of São Paulo, Brazil, along 20 years (2000-2019). Among the non-susceptible isolates, 31.55, 14.06, and 13.18% were resistant to aminoglycosides, tetracycline, and β-lactams, respectively. Moreover, 68 and 11 isolates were considered MDR and Extended Spectrum β-Lactamase (ESBL) producers, respectively, whereas one isolate was colistin-resistant. We selected four strains to obtain a draft of the Genome Sequence; one S. Infantis (ST32), one S. Enteritidis (ST11), one S. I 4,[5],12:i:- (ST19), and one S. Typhimurium (ST313). Among them, three presented at least one of the following antimicrobial resistance genes (AMR) linked to mobile DNA: blaTEM-1B, dfrA1, tetA, sul1, floR, aac(6')-laa, and qnrE1. This is the first description of the plasmid-mediated quinolone resistance (PMQR) gene qnrE1 in a clinical isolate of S. I 4,[5],12:i:-. The S. Typhimurium is a colistin-resistant isolate, but did not harbor mcr genes, but it presented mutations within the mgrB, pmrB, and pmrC regions that might be linked to the colistin-resistant phenotype. The virulence pattern of the four isolates resembled the virulence pattern of the highly pathogenic S. Typhimurium UK-1 reference strain in assays involving the in vivo Galleria mellonella model. In conclusion, most isolates studied here are susceptible, but a small percentage present an MDR or ESBL-producer and pathogenic phenotype. Sequence analyses revealed plasmid-encoded AMR genes, such as β-lactam and fluoroquinolone resistance genes, indicating that these characteristics can be potentially disseminated among other bacterial strains.

Emergence, Dissemination and Antimicrobial Resistance of the Main Poultry-Associated Salmonella Serovars in Brazil

Salmonella infects poultry, and it is also a human foodborne pathogen. This bacterial genus is classified into several serovars/lineages, some of them showing high antimicrobial resistance (AMR). The ease of Salmonella transmission in farms, slaughterhouses, and eggs industries has made controlling it a real challenge in the poultry-production chains. This review describes the emergence, dissemination, and AMR of the main Salmonella serovars and lineages detected in Brazilian poultry. It is reported that few serovars emerged and have been more widely disseminated in breeders, broilers, and layers in the last 70 years. Salmonella Gallinarum was the first to spread on the farms, remaining as a concerning poultry pathogen. Salmonella Typhimurium and Enteritidis were also largely detected in poultry and foods (eggs, chicken, turkey), being associated with several human foodborne outbreaks. Salmonella Heidelberg and Minnesota have been more widely spread in recent years, resulting in frequent chicken/turkey meat contamination. A few more serovars (Infantis, Newport, Hadar, Senftenberg, Schwarzengrund, and Mbandaka, among others) were also detected, but less frequently and usually in specific poultry-production regions. AMR has been identified in most isolates, highlighting multi-drug resistance in specific poultry lineages from the serovars Typhimurium, Heidelberg, and Minnesota. Epidemiological studies are necessary to trace and control this pathogen in Brazilian commercial poultry production chains.

Molecular genotyping reveals inter-regional relatedness among antimicrobial resistant Salmonella Minnesota strains isolated from poultry farm and humans, Brazil

Genetic profiles of Salmonella Minnesota isolates were analyzed using pulsed-field gel electrophoresis (PFGE). In total, 13 isolates obtained from the broiler industry collected in the states of Minas Gerais (11) and São Paulo (2), as well as five recovered from cases of foodborne infections in humans in the states of Minas Gerais (2), Santa Catarina (1), and Rio Grande do Sul (2), were submitted to PFGE. These 18 S. Minnesota isolates together with other 12 of poultry origin were also subjected to antimicrobial susceptibility testing. The PFGE analysis of 18 strains of S. Minnesota generated a dendrogram that grouped the isolates with 83-90% similarity into four main clusters. Among them, cluster "A" grouped the majority of isolates (13), including two of human origin that showed 90% similarity with a broiler isolate, both recovered in Minas Gerais. The S. Minnesota isolates showed resistance to tetracycline (80%), cefoxitin (80%), ceftazidime (46.7%), nalidixic acid (23.3%), ciprofloxacin (13.3%), and streptomycin (10%). No resistance to gentamicin, chloramphenicol, meropenem, nitrofurantoin, and sulfamethoxazole-trimethoprim was found. Moreover, 23.3% of the evaluated isolates presented multi-resistance profile, all from Minas Gerais. The results highlight the importance of further studies involving S. Minnesota, which is prevalent in the Brazilian broiler flocks and could provoke foodborne infection in humans.

Molecular characterization of Salmonella spp. and Listeria monocytogenes strains from biofilms in cattle and poultry slaughterhouses located in the federal District and State of Goiás, Brazil

Listeria monocytogenes and Salmonella spp. are considered important foodborne pathogens that are commonly associated with foods of animal origin. The aim of this study was to perform molecular characterization of L. monocytogenes and Salmonella spp. isolated from biofilms of cattle and poultry slaughterhouses located in the Federal District and State of Goiás, Brazil. Fourteen L. monocytogenes isolates and one Salmonella sp. were detected in poultry slaughterhouses. No isolates were detected in cattle slaughterhouses. All L. monocytogenes isolates belonged to lineage II, and 11 different pulsotypes were detected. Pulsed-field gel electrophoresis analysis revealed the dissemination of two strains within one plant, in addition to the regional dissemination of one of them. The Salmonella isolate was identified via whole genome sequencing as Salmonella enterica serovar Minnesota ST548. In the sequence analysis, no premature stop codons were detected in the inlA gene of Listeria. All isolates demonstrated the ability to adhere to Caco-2 cells, while 50% were capable of invading them. Antimicrobial resistance was detected in 57.1% of the L. monocytogenes isolates, and resistance to sulfonamide was the most common feature. The tetC, ermB, and tetM genes were detected, and four isolates were classified as multidrug-resistant. Salmonella sp. was resistant to nine antimicrobials and was classified as multidrug-resistant. Resistance genes qnrB19, blaCMY-2, aac(6')-Iaa, sul2, and tetA, and a mutation in the parC gene were detected. The majority (78.5%) of the L. monocytogenes isolates were capable of forming biofilms after incubation at 37°C for 24 h, and 64.3% were capable of forming biofilms after incubation at 12°C for 168 h. There was no statistical difference in the biofilm-forming capacity under the different evaluated conditions. Salmonella sp. was capable of forming biofilms at both tested temperatures. Biofilm characterization was confirmed by collecting the samples consistently, at the same sampling points, and by assessing biofilm formation in vitro. These results highlight the potential risk of cross-contamination in poultry slaughterhouses and the importance of surveillance and pathogen control maintenance programs within the meat production industry.

Exogenous Citrulline and Glutamine Contribute to Reverse the Resistance of Salmonella to Apramycin

Antibiotic resistance is an increasing concern for human and animal health worldwide. Recently, the concept of reverting bacterial resistance by changing the metabolic state of antibiotic-resistant bacteria has emerged. In this study, we investigated the reversal of Apramycin resistance in Salmonella. First, non-targeted metabonomics were used to identify key differential metabolites of drug-resistant bacteria. Then, the reversal effect of exogenous substances was verified in vivo and in vitro. Finally, the underlying mechanism was studied. The results showed that the metabolites citrulline and glutamine were significantly reduced in Apramycin-resistant Salmonella. When citrulline and glutamine were added to the culture medium of drug-resistant Salmonella, the killing effect of Apramycin was restored markedly. Mechanistic studies showed that citrulline and glutamine promoted the Tricarboxylic acid cycle, produced more NADH in the bacteria, and increased the proton-motive force, thus promoting Apramycin entry into the bacterial cells, and killing the drug-resistant bacteria. This study provides a useful method to manage infections by antibiotic-resistant bacteria.

Prevalence, main serovars and anti-microbial resistance profiles of non-typhoidal Salmonella in poultry samples from the Americas: A systematic review and meta-analysis

Poultry and poultry-derived products such as meat and eggs are among the main sources of non-typhoidal Salmonella (NTS) transmission to humans. Therefore, we performed a systematic review and used random-effects meta-analyses to (1) estimate the prevalence of NTS in poultry samples from birds, products and subproducts and environmental samples, (2) examine the diversity and frequency of their serovars and (3) estimate the prevalence and profiles of anti-microbial resistance (AMR) in NTS isolates reported in studies from the Americas. We included 157 studies from 15 countries comprising 261,408 poultry samples and estimated an overall pooled prevalence of 17.9% (95% Confidence Interval: 10.8-26.3) in birds, 21.8% (17.7-26.1) in products and subproducts and 29.5% (24.2-35.1) in environmental samples. At the national level, the prevalence of NTS was heterogeneous across countries with the highest values in Mexico, the United States and Canada. In total, 131 serovars were identified from 13,388 isolates; Heidelberg, Kentucky, Enteritidis and Typhimurium were the most prevalent in the overall top 10 ranking (range 6.5%-20.8%). At the national level, Enteritidis and Typhimurium were identified in most of the countries, though with national differences in their ranks. The prevalence of AMR increased from 24.1% for 1 antibiotic to 36.2% for 2-3 antibiotics and 49.6% for ≥ 4 antibiotics. Kentucky, Heidelberg, Typhimurium and Enteritidis were the serovars with the highest prevalence of AMR. Besides, tetracycline, ampicillin, streptomycin, ceftiofur and amoxicillin-clavulanic acid were the most frequent antibiotics to which NTS showed resistance. In conclusion, NTS was distributed through the avian production chain with high and heterogeneous values of prevalence in poultry samples. Besides, there were distinctive patterns of serovars distribution across countries and an alarming prevalence of AMR among zoonotic serovars.

Presence of Tetracycline and Sulfonamide Resistance Genes in Salmonella spp.: Literature Review

Tetracyclines and sulfonamides are broad-spectrum antibacterial agents which have been used to treat bacterial infections for over half a century. The widespread use of tetracyclines and sulfonamides led to the emergence of resistance in a diverse group of bacteria. This resistance can be studied by searching for resistance genes present in the bacteria responsible for different resistance mechanisms. Salmonella is one of the leading bacteria causing foodborne diseases worldwide, and its resistance to tetracyclines and sulfonamides has been widely reported. The literature review searched the Virtual Health Library for articles with specific data in the studied samples: the resistance genes found, the primers used in PCR, and the thermocycler conditions. The results revealed that Salmonella presented high rates of resistance to tetracycline and sulfonamide, and the most frequent samples used to isolate Salmonella were poultry and pork. The tetracycline resistance genes most frequently detected from Salmonella spp. were tetA followed by tetB. The gene sul1 followed by sul2 were the most frequently sulfonamide resistance genes present in Salmonella. These genes are associated with plasmids, transposons, or both, and are often conjugative, highlighting the transference potential of these genes to other bacteria, environments, animals, and humans.

Genomic Characterization of a Nalidixic Acid-Resistant Salmonella Enteritidis Strain Causing Persistent Infections in Broiler Chickens

Virulent strains of Salmonella enterica subsp. enterica serovar Enteritidis (SE) harbored by poultry can cause disease in poultry flocks and potentially result in human foodborne illness. Two broiler flocks grown a year apart on the same premises experienced mortality throughout the growing period due to septicemic disease caused by SE. Gross lesions predominantly consisted of polyserositis followed by yolk sacculitis, arthritis, osteomyelitis, and spondylitis. Tissues with lesions were cultured yielding 59 SE isolates. These were genotyped by Rep-PCR followed by whole-genome sequencing (WGS) of 15 isolates which were clonal. The strain, SE_TAU19, was further characterized for antimicrobial susceptibility and virulence in a broiler embryo lethality assay. SE_TAU19 was resistant to nalidixic acid and sulfadimethoxine and was virulent to embryos with 100% mortality of all challenged broiler embryos within 3.5 days. Screening the SE_TAU19 whole-genome sequence revealed seven antimicrobial resistance (AMR) genes, 120 virulence genes, and two IncF plasmid replicons corresponding to a single, serovar-specific pSEV virulence plasmid. The pef, spv, and rck virulence genes localized to the plasmid sequence assembly. We report phenotypic and genomic features of a virulent SE strain from persistently infected broiler flocks and present a workflow for SE characterization from isolate collection to genome assembly and sequence analysis. Further SE surveillance and investigation of SE virulence in broiler chickens is warranted.

Monitoring of Antimicrobial Susceptibility of Bacteria Isolated from Poultry Farms from 2014 to 2018

The current situation of antibiotic resistance of most bacterial pathogens was a threat to the poultry and public health with increasing economic losses. Regarding this problem, monitoring of the circulating microorganisms occurred with the antibiotic resistance profile. A total of 657 different samples from internal organs (liver, heart, lung, and yolk) and paper-lining chick boxes were collected from native chicken farms which were submitted to the Reference Laboratory for Veterinary Quality Control on Poultry Production in the period from 2014 to 2018 for the detection of Salmonella, Escherichia coli (E. coli), and Staphylococcus. The bacterial isolates were tested for their antimicrobial susceptibility by disk diffusion technique. Salmonella was isolated from 128 out of 657 (19.5%), E. coli was isolated from 496 out of 657 (75.5%), and Staphylococcus species was isolated from 497 out of 657 (75.6%). All Salmonella positive samples were examined for antibiotic resistance against 10 different antibiotics, and the highest percentage all over the five years was against penicillin, ampicillin, and tetracycline. All E. coli positive samples were examined for antibiotic resistance against 14 different antibiotics, and the highest percentage all over the five years was with ampicillin, tetracycline, norfloxacin, streptomycin, and danofloxacin. All Staphylococcus positive sample species were examined for antibiotic resistance against 14 different antibiotics, and the highest percentage of resistance all over the five years was shown with tetracycline, streptomycin, ampicillin, and nalidixic acid.

Occurrence of Escherichia coli and Salmonella species in Some Livestock (Poultry) Feeds in Mando, Kaduna, Nigeria

The study aimed at assessing the proximate composition, isolation, characterization of some Enterobacteriaceae from two (2) brands of poultry feeds marketed in Mando, Kaduna, Nigeria. A total of sixteen (16) samples of two (2) different poultry feeds (starter and finisher) from four (4) poultry farms in mando were collected and subjected to proximate and microbiological analysis. The proximate analysis was carried out using standard techniques and procedures. All the feed samples were cultured on separate media which include Eosin methylene blue (EMB), nutrient Agar (NA) and Salmonella-Shigella Agar (SSA) media using standard procedures. The antibiogram of the selected antibiotics was evaluated against the test isolates. The result of proximate analysis of the starter and finisher feeds indicated that the Dry matter of starter feed had the highest percentage composition of 95.02% and crude fiber of the finisher feed had the lowest composition of 3.78%. The highest number of bacterial load was recorded to be 10.0×104 CFU/g for the feed sample A (starter feed) and 12.0x104CFU/g was recorded for the feed sample B (finisher feed) which had the highest number of bacterial load recorded among the two (2) different poultry feeds analyzed. The bacteria isolates were identified as Salmonella species and Escherichia coli. Total viable count (TVC) of Salmonella species and E. coli in the feed samples (starter and finisher) ranges from 3.0×104CFU/g to 12.0×104CFU/g. Both organisms (Salmonella species, E. coli) were found as 37.5% and 25% of the analyzed feeds (Broiler starter and broiler finisher) samples, respectively. There was no level of significant (p>0.05) difference between the level of contamination of Salmonella species and E. coli in the two different feeds analyzed, as p=0.06 and p=0.13 for Salmonella species, and E. coli respectively. Sample A and B (Starter and Finisher) feeds had the highest number of Salmonella species occurrence with six ( 6) positive samples while E. coli was recorded in four (4) samples of A and B (Starter and Finisher) feeds. The result of the antibiogram indicated that ciprofloxacin (30 µg), Gentamycin (30µg), Perfloxacin (30µg) and Tarvid (30µg) was effective against Salmonella species and Escherichia coli. The significant of spread of the species of the Enterobacteriaceae in livestock feeds requires the need for effective quality assurance and control, good hygiene practices in production and proper handling of the poultry feeds.

Mechanistic Insight into Antimicrobial and Antioxidant Potential of Jasminum Species: A Herbal Approach for Disease Management

Drug resistance among microbial pathogens and oxidative stress caused by reactive oxygen species are two of the most challenging global issues. Firstly, drug-resistant pathogens cause several fatalities every year. Secondly aging and a variety of diseases, such as cardiovascular disease and cancer, are associated with free radical generated oxidative stress. The treatments currently available are limited, ineffective, or less efficient, so there is an immediate need to tackle these issues by looking for new therapies to resolve resistance and neutralize the harmful effects of free radicals. In the 21st century, the best way to save humans from them could be by using plants as well as their bioactive constituents. In this specific context, Jasminum is a major plant genus that is used in the Ayurvedic system of medicine to treat a variety of ailments. The information in this review was gathered from a variety of sources, including books, websites, and databases such as Science Direct, PubMed, and Google Scholar. In this review, a total of 14 species of Jasminum have been found to be efficient and effective against a wide variety of microbial pathogens. In addition, 14 species were found to be active free radical scavengers. The review is also focused on the disorders related to oxidative stress, and it was concluded that Jasminum grandiflorum and J. sambac normalized various parameters that were elevated by free radical generation. Alkaloids, flavonoids (rutoside), terpenes, phenols, and iridoid glucosides are among the main phytoconstituents found in various Jasminum species. Furthermore, this review also provides insight into the mechanistic basis of drug resistance, the generation of free radicals, and the role of Jasminum plants in combating resistance and neutralizing free radicals.

Serotyping and Antimicrobial Resistance Profile of Enteric Nontyphoidal Salmonella Recovered from Febrile Neutropenic Patients and Poultry in Egypt

A total of 300 human fecal samples were collected from febrile neutropenic patients suffering from severe gastroenteritis, followed by identification and serological characterization of recovered isolates. Fifty nontyphoidal Salmonella (NTS) serovars were recovered. A total of serologically identified 50 NTS serovars recovered from poultry of the same geographical area and during the same period as well as one standard strain S. Poona were supplied by the Bacterial Bank of Animal Health Research Institute of Egypt. Antibiogram analysis revealed that the human and poultry serovars exhibited similar antimicrobial resistance patterns against 28 different antimicrobial agents, particularly against ampicillin, cefotaxime, oxytetracycline, and erythromycin. Plasmids harboring blaCTX-m, blaSHV, blaTEM, and aac(6')-Ib were detected in 11 (22%) and 8 (16%) of human and poultry serovars, respectively. Molecular detection of the most clinically relevant virulence genes and analysis of the associated virulence genotypes proved that the human (n = 11) and poultry serovars (n = 12) shared 11 genotypes. Enterobacterial repetitive intergenic consensus PCR analysis revealed that human and poultry serovars were clustered together in 3 out of the 4 clusters with a similarity index ranged from 0.15 to 1. Since poultry are usually consumed by humans, the presence of resistant bacteria harboring transmissible genetic elements is of great health concern.

Antimicrobial resistance of Salmonella from poultry meat in Brazil: results of a nationwide survey

The use of antimicrobials in food-producing animals can lead to increased bacterial resistance. Important information to address this problem can be provided by monitoring antimicrobial resistance (AMR) in foodborne pathogens. As part of preliminary activities for the implementation of AMR surveillance in Brazil, a nationwide survey on AMR in Salmonella enterica isolates from poultry meat was conducted. The survey evaluated 146 Salmonella isolates from poultry meat in 2014, and 163 isolates obtained in 2017. Minimal inhibitory concentrations of 13 antimicrobials were determined by broth microdilution, and isolates were assigned to serotypes by automated ribotyping. High resistance rates were found in 2014 and 2017, in particular to nalidixic acid (84/146, 57.5% and 141/163, 86.5%, respectively), ampicillin (82/146, 56.2% and 125/163, 76.7%), cefotaxime (76/146, 52.1% and 124/163, 76.1%), ceftazidime (73/146, 50.0% and 124/163, 76.1%), ciprofloxacin (83/146, 56.9% and 145/163, 89.0%) and tetracycline (88/146, 60.3% and 135/163, 82.8%). There was a significant increase in resistance to these antibiotics in the second survey period. Salmonella ser. Heidelberg and Salmonella ser. Minnesota were the main serotypes expressing resistance to these antimicrobials. Multidrug resistance was found in 50.7% (74/146) of the isolates from 2014, and in 77.3% (126/163) of isolates from 2017 (P < 0.05). None of the isolates was resistant to azithromycin or meropenem. These findings indicate high and increasing rates of resistance among Salmonella from poultry meat in Brazil, mainly associated with Salmonella ser. Heidelberg and Salmonella ser. Minnesota, stressing the importance of continuous monitoring of AMR in the poultry chain.

Epidemiology of streptomycin resistant Salmonella from humans and animals in Ethiopia: A systematic review and meta-analysis

BACKGROUND

Streptomycin is used as an epidemiological marker in monitoring programs for antimicrobial resistance in Salmonella serovars and indicates the presence of pentaresistance. However, comprehensive data on streptomycin resistant Salmonella among human, animal, and animal products is lacking in Ethiopia. In this review, we aimed to assess heterogeneity and pooled proportion of Salmonella serovars to streptomycin resistance among human, animal and animal products in Ethiopia.

METHODS

We conducted a systematic review and meta-analysis of published literature from Ethiopia. We used the MEDLINE/ PubMed, Embase, Cochrane Library, and Google Scholar databases to identify genetic and phenotypic data on Salmonella isolates. To determine the heterogeneity and pooled proportion, we used metaprop commands and the random-effects model. Relative and cumulative frequencies were calculated to describe the overall preponderance of streptomycin resistance isolates after arcsine-transformed data. Metan funnel and meta-bias using a begg test were performed to check for publication bias.

RESULTS

Overall, we included 1475 Salmonella serovars in this meta-analysis. The pooled proportion of streptomycin resistance was 47% (95% CI: 35-60%). Sub-group analysis by target population showed that the proportion of streptomycin resistance in Salmonella serovars was 54% (95% CI: 35-73%) in animal, 44% (95% Cl: 33-59%) in humans and 39% (95% CI: 24-55%) in animals products. The streptomycin resistant Salmonella serovars were statistically increasing from 0.35(95% CI: 0.12-0.58) in 2003 to 0.77(95% CI: 0.64-0.89) in 2018. The level of multidrug-resistant (MDR) Salmonella serovars was 50.1% in the meta-analysis.

CONCLUSION

We found a high level of streptomycin resistance, including multidrug, Salmonella serovars among human, animals, and animal products. This resistance was significantly increasing in the last three decades (1985-2018). The resistance to streptomycin among Salmonella serovars isolated from animals was higher than humans. This mandates the continuous monitoring of streptomycin use and practicing one health approach to preventing further development of resistance in Ethiopia.

REGISTRATION

We conducted a systematic review and meta-analysis after registration of the protocol in PROSPERO (CRD42019135116) following the MOOSE (Meta-Analysis of Observational Studies in Epidemiology).

Antimicrobial resistance and related gene analysis of Salmonella from egg and chicken sources by whole-genome sequencing

Whole-genome sequencing (WGS) is a valuable tool in research on foodborne pathogens. In this study, a total of 143 isolates of Salmonella serotypes Enteritidis, Typhimurium, and Heidelberg sourced from eggs and chickens were analyzed for their antimicrobial resistance profiles using WGS data. The isolates carried high rate of genes resistant to aminoglycoside (70.63%), tetracycline (26.57%), fosfomycin (25.17%), sulfonamides (23.78%), and β-lactamases (15.38%); and aadA was the most frequently observed antimicrobial resistance gene (ARG). Antimicrobial resistance varies by Salmonella serotypes, with Salmonella enterica serovar Enteritidis (Salmonella ser. Enteritidis) isolates being highly resistant to aminoglycoside (particularly streptomycin); Salmonella ser. Typhimurium more resistant to aminoglycoside, tetracycline, and sulfonamides; and Salmonella ser. Heidelberg more resistant to aminoglycoside and fosfomycin. Salmonella ser. Typhimurium isolates presented more varieties of ARG than Salmonella ser. Enteritidis and Salmonella ser. Heidelberg. Our data showed that 5 isolates of Salmonella ser. Typhimurium and Salmonella ser. Heidelberg contained ARG resistant to ≥ 5 antimicrobials. In addition, 23 Salmonella isolates carried ARG resistant to 4 antimicrobials.

Prevalence, Distribution, and Diversity of Salmonella Strains Isolated From a Subtropical Lake

This study investigated the prevalence, serovar distribution, antimicrobial resistance, and pulsed field gel electrophoresis (PFGE) typing of Salmonella enterica isolated from Lake Zapotlán, Jalisco, Mexico. Additionally, the association of the presence of Salmonella with physicochemical and environmental parameters was analyzed using Pearson correlation analysis and principal component analysis (PCA). Salmonella spp. were identified in 19 of 63 (30.15%) samples. The prevalence of Salmonella was positively correlated with air temperature, electrical conductivity, pH, and dissolved oxygen and negatively correlated with relative humidity, water temperature, turbidity, and precipitation. The predominant serotype identified was Agona (68.48%), followed by Weltevreden (5.26%), Typhimurium (5.26%), and serogroup B (21.05%). Overall, the highest detected antimicrobial resistance was toward colistin (73.68%), followed by sulfamethoxazole (63.15%), tetracycline (57.89%), nalidixic acid (52.63%), and trimethoprim (52.63%). All Salmonella strains were genetically diverse, with a total of 11 XbaI and four BlnI profiles on PFGE. The use of these two enzymes allowed differentiate strains of Salmonella of the same serotype. The results obtained in this study contribute to a better understanding of the Salmonella spp. ecology in an endorheic subtropical lake and provide information for decision makers to propose and implement effective strategies to control point and non-point sources of pathogen contamination.

Evaluation of Antioxidant, Antimicrobial and Tyrosinase Inhibitory Activities of Extracts from Tricholosporum goniospermum, an Edible Wild Mushroom

Tricholosporum goniospermum (Bres.) Guzmán ex T.J. Baroni is an excellent edible mushroom whose compounds and biological properties are still unknown. In this study, n-hexane, ethyl acetate and methanol extracts from fruiting bodies and liquid-cultured mycelia were compared for the analysis of phenolic compounds, the evaluation of scavenger (DPPH, ABTS) and reducing (CUPRAC, FRAP) activities, and the enzyme inhibition of α-amylase, acetylcholinesterase (AChE), butyrylcholinesterase (BChE) and tyrosinase. Additionally, T. goniospermum extracts were evaluated for antibacterial and antimycotic activities against Gram+ and Gram- bacteria, and clinical yeast and fungal dermatophytes. Finally, based on the extract content in phenolic compounds, in silico studies, including the docking approach, were conducted to predict the putative targets (namely tyrosinase, lanosterol-14-α-demethylase, the multidrug efflux system transporters of E. coli (mdtK) and P. aeruginosa (pmpM), and S. aureus β-lactamase (ORF259)) underlying the observed bio-pharmacological and microbiological effects. The methanolic extract from mycelia was the richest in gallic acid, whereas the ethyl acetate extract from fruiting bodies was the sole extract to show levels of catechin. Specifically, docking runs demonstrated an affinity of catechin towards all docked proteins, in the micromolar range. These in silico data are consistent, at least in part, with the highest activity of ethyl acetate extract as an antimicrobial and anti-tyrosinase (554.30 mg KAE/g for fruiting bodies and 412.81 mg KAE/g for mycelia) agent. The ethyl acetate extracts were also noted as being the most active (2.97 mmol ACAE/g for fruiting bodies and 2.25 mmol ACAE/g for mycelia) on α-amylase. BChE inhibitory activities varied from 2.61 to 26.78 mg GALAE/g, while the tested extracts were not active on AChE. In conclusion, all mushroom extracts tested in this study had potent antimicrobial activities. Particularly, among the tested extracts, the ethyl acetate extract showed the highest efficacy as both an antimicrobial and anti-tyrosinase agent. This could be related, albeit partially, to its content of catechin. In this regard, the bioinformatics analyses showed interactions of catechin with tyrosinase and specific microbial proteins involved in the resistance to chemotherapeutic drugs, thus suggesting innovative pharmacological applications of T. goniospermum extracts.

Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades

Salmonella is a leading human pathogen and a significant public health concern worldwide. Massive food production and distribution have contributed to this pathogen dissemination, which, combined with antimicrobial resistance (AMR), creates new control challenges in food safety. The development of AMR is a natural phenomenon and can occur in the bacterial evolutionary process. However, the overuse and the misuse of antimicrobial drugs in humans and in animals have increased AMR selective pressure. In Brazil, there is an accuracy lack in AMR frequency in Salmonella because too many isolates are under-investigated for genetic and phenotypic AMR by the Brazilian health authorities and the research community. This underreporting situation makes the comprehension of the real level of Salmonella AMR in the country difficult. The present study aimed to use bioinformatics tools for a rapid in silico screening of the genetic antimicrobial resistance profile of Salmonella through whole-genome sequences (WGS). A total of 930 whole-genome sequences of Salmonella were retrieved from the public database of the National Biotechnology Information Center (NCBI). A total of 65 distinct resistance genes were detected, and the most frequent ones were tet(A), sul2, and fosA7. Nine point mutations were detected in total, and parC at the 57 position (threonine → serine) was the highest frequent substitution (26.7%, 249/930), followed by gyrA at the 83 position (serine → phenylalanine) (20.0%, 186/930) and at the 87 position (aspartic acid → asparagine) (15.7%, 146/930). The in silico prediction of resistance phenotype showed that 58.0% (540/930) of the strains can display a multidrug resistance (MDR) profile. Ciprofloxacin and nalidixic acid were the antimicrobial drugs with the highest frequency rates of the predicted phenotype resistance among the strains. The temporal analysis through the last four decades showed increased frequency rates of antimicrobial resistance genes and predicted resistance phenotypes in the 2000s and the 2010s when compared with the 1980s and 1990s. The results presented herein contributed significantly to the understanding of the strategic use of WGS associated with in silico analysis and the predictions for the determination of AMR in Salmonella from Brazil.

Prevalence of Salmonella and Campylobacter spp. in Alternative and Conventionally Produced Chicken in the United States: A Systematic Review and Meta-Analysis

ABSTRACT

The burden of foodborne illness linked to the consumption of contaminated broiler meat is high in the United States. With the increase in popularity of alternative poultry rearing and production systems, it is important to identify the differences in food safety risks presented by alternative systems compared with conventional methods. Although many studies have been conducted that surveyed foodborne pathogen prevalence along the broiler supply chain, a systematic overview of all of the results is lacking. In the current study, a systematic review and meta-analysis were conducted to quantify the differences in prevalence of Salmonella and Campylobacter spp. in farm environment, rehang, prechill, postchill, and retail samples between conventional and alternative production systems. A systematic search of Web of Science and PubMed databases was conducted to identify eligible studies. Studies were then evaluated by inclusion criteria, and the included studies were qualitatively and quantitatively analyzed. In total, 137 trials from 72 studies were used in the final meta-analysis. Meta-analysis models were individually constructed for subgroups that were determined by sample type, pathogen, and production type. All subgroups possessed high amounts of heterogeneity (I2 > 75%). For environmental sample subgroups, Campylobacter prevalence was estimated to be 15.8 and 52.8% for conventional and alternative samples, respectively. Similar prevalence estimates for both production types were observed for Salmonella environmental samples and all retail samples. For conventional samples, Campylobacter and Salmonella prevalence was highest in prechill samples followed by rehang and postchill samples, respectively. The results herein will be useful in future quantitative microbial risk assessments for characterizing the differences in foodborne illness risks presented by different broiler production systems.

HIGHLIGHTS

Closed Genome Sequences and Antimicrobial Resistance Profiles of Eight Wild Bird Salmonella Isolates Obtained with MinION and Illumina MiSeq Sequencing

Complete genome sequences of eight isolates of Salmonella enterica subsp. enterica from Canadian wild birds were determined by MinION and Illumina MiSeq sequencing. Assembled chromosomes had an average size of 4,833,662 bp. Salmonella enterica serovar Worthington obtained from partridge and quail carried 267-kb plasmids, which contained multiple antimicrobial resistance genes.

Complete genome sequences of eight isolates of Salmonella enterica subsp. enterica from Canadian wild birds were determined by MinION and Illumina MiSeq sequencing. Assembled chromosomes had an average size of 4,833,662 bp. Salmonella enterica serovar Worthington obtained from partridge and quail carried 267-kb plasmids, which contained multiple antimicrobial resistance genes.

Antimicrobial Resistance in Nontyphoidal Salmonella Isolates from Human and Swine Sources in Brazil: A Systematic Review of the Past Three Decades

Salmonella is the leading cause of foodborne illnesses worldwide. The widespread use of antimicrobials as prophylactic, therapeutic, and growth promoters in both livestock and human medicine has resulted in selective pressure regarding antimicrobial-resistant (AMR) bacteria. This systematic review summarizes phenotypic antimicrobial resistance profiles in Salmonella isolates from human and swine sources between 1990 and 2018 in Brazil. The 20 studies that matched the eligibility criteria-isolates from pigs and humans from Brazil, between 1990 and 2016, containing information on the number of Salmonella isolates, and applying the disk diffusion susceptibility method-were included. During the assessed period, Salmonella strains isolated from swine sources displayed the highest resistance rates for tetracycline (20.3%) and sulfonamides (17.4%). In contrast, human isolates displayed the highest resistance rates against ampicillin (19.8%) and tetracycline (17%). Salmonella Typhimurium was the most frequent AMR isolate from both swine and human sources, corresponding to 67% of all isolates. From 2001 to 2005, tetracycline and ampicillin were the top antimicrobial resistance compounds, and the most frequently detected in swine and human sources, respectively. A total of 63 and 58 multiple drug resistance profiles were identified in swine and human isolates, respectively. Antimicrobial resistance has decreased throughout the 1990-2016 period, except for gentamicin and nalidixic acid in swine and human isolates, respectively. The results indicate that Salmonella isolated from human and swine display resistance against clinically important antimicrobials, indicating that swine are possibly one of the main vectors for spreading human salmonellosis in Brazil.

Bonelli R, A. Penna B, P. Albuquerque J, M. Souza R, M. F. Cerqueira A. Antimicrobial Resistance in Farm Animals in Brazil: An Update Overview

In animal husbandry, antimicrobial agents have been administered as supplements to increase production over the last 60 years. Large-scale animal production has increased the importance of antibiotic management because it may favor the evolution of antimicrobial resistance and select resistant strains. Brazil is a significant producer and exporter of animal-derived food. Although Brazil is still preparing a national surveillance plan, several changes in legislation and timely programs have been implemented. Thus, Brazilian data on antimicrobial resistance in bacteria associated with animals come from official programs and the scientific community. This review aims to update and discuss the available Brazilian data on this topic, emphasizing legal aspects, incidence, and genetics of the resistance reported by studies published since 2009, focusing on farm animals and derived foods with the most global public health impact. Studies are related to poultry, cattle, and pigs, and mainly concentrate on non-typhoid Salmonella, Escherichia coli, and Staphylococcus aureus. We also describe legal aspects of antimicrobial use in this context; and the current occurrence of genetic elements associated with resistance to beta-lactams, colistin, and fluoroquinolones, among other antimicrobial agents. Data here presented may be useful to provide a better understanding of the Brazilian status on antimicrobial resistance related to farm animals and animal-derived food products.

Antimicrobial Resistance in Farm Animals in Brazil: An Update Overview

In animal husbandry, antimicrobial agents have been administered as supplements to increase production over the last 60 years. Large-scale animal production has increased the importance of antibiotic management because it may favor the evolution of antimicrobial resistance and select resistant strains. Brazil is a significant producer and exporter of animal-derived food. Although Brazil is still preparing a national surveillance plan, several changes in legislation and timely programs have been implemented. Thus, Brazilian data on antimicrobial resistance in bacteria associated with animals come from official programs and the scientific community. This review aims to update and discuss the available Brazilian data on this topic, emphasizing legal aspects, incidence, and genetics of the resistance reported by studies published since 2009, focusing on farm animals and derived foods with the most global public health impact. Studies are related to poultry, cattle, and pigs, and mainly concentrate on non-typhoid Salmonella, Escherichia coli, and Staphylococcus aureus. We also describe legal aspects of antimicrobial use in this context; and the current occurrence of genetic elements associated with resistance to beta-lactams, colistin, and fluoroquinolones, among other antimicrobial agents. Data here presented may be useful to provide a better understanding of the Brazilian status on antimicrobial resistance related to farm animals and animal-derived food products.

Evaluation of in-vivo anti-Salmonella activity of Uvaria chamae, Lantana camara and Phyllantus amarus used in Benin, West Africa

BACKGROUND

Uvaria chamae (Annonaceae), Phyllantus amarus (Phyllantaceae) and Lantana camara (Verbenaceae) are empirically alleged to be used as Beninese medicinal plants in the treatment of salmonellosis. This study aimed to produce scientific data on in vitro and in vivo efficacy of Uvaria chamae, Lantana camara and Phyllantus amarus on multiresistant Salmonella spp isolated in Benin.

RESULTS

After performing in vitro tests on aqueous and ethanolic extracts of these plants, only the aqueous extract of Uvaria chamae (leaves) showed the best anti-Salmonella's activity and was used for this in vivo experiment. The induction of salmonellosis revealed 9 × 108 CFU/ml was the optimal concentration triggering and maintaining symptoms in chicks. This infective concentration was used for in vivo assessment. Twenty-four hours post inoculation, the symptoms of salmonellosis (wet cloaca, diarrhea stools and somnolence) were observed in infected groups. After 7 days of treatment, the reduction of bacterial load at 100 mg/L, 200 mg/L, 400 mg/L of the extract was respectively 85%, 52.38% and 98% for Uvaria chamae, Phyllantus amarus and Lantana camara in the chick's groups infected with Salmonella Typhimurium ATCC 14028. On the other hand, colistin completely cancelled the bacterial load (reduction rate of 100%). With the groups infected with Salmonella spp (virulent strain), the reduction rate of bacterial load at 100 mg/L, 200 mg/L, 400 mg/L of extract was 0%, 98.66%, and 99.33%. The extracts at 200 and 400 mg/L were more active than colistin, which reduced the bacterial load by 33.33%. The toxicity tests did not show any negative effect of Colistin and the Uvaria chamae's extract on the biochemical and hematological parameters of the chicks.

CONCLUSION

The aqueous extract of Uvaria chamae is active in vitro and in vivo on multiresistant strains of Salmonella enterica. This plant is a good candidate for the development of an improved traditional medicine for the management of salmonellosis.

Diversity of Serotype, Genotype, and Antibiotic Susceptibility of Salmonella Prevalent in Pickled Ready-to-Eat Meat

Pickled ready-to-eat meat (PRTEM) is a meat product that is treated with various seasonings and then cooked. PRTEM is a popular food consumed mostly in China and some Asian countries. Since this food is considered 'ready to eat', once it is contaminated by foodborne pathogens such as Salmonella, the prospect for significant morbidity, mortality, and immeasurable economic losses can occur. Here we investigated the prevalence and concentration of Salmonella in 107 PRTEM samples collected from Shaanxi, China during 2015-2016. Furthermore, we analyzed the serotype, antibiotic susceptibility, and presence of antibiotic resistance genes and amino acid mutations in 219 Salmonella isolates, followed by subtyping of 115 representative isolates. The average detection rate of Salmonella-positive PRTEM was 58.9%, and the average most probable number (MPN) of Salmonella in positive samples was 2.27 logMPN per gram of sample (range: 2.10-2.43). Ten serotypes were identified from the 219 Salmonella isolates, with S. Thompson (37.9%) and S. Indiana (20.5%) being predominant. The remaining serotypes were S. Typhi (7.8%), S. Typhimurium (7.3%), S. Mbandaka (6.9%), S. Albany (6.4%), S. Blockley (5.5%), S. Infantis (4.1%), S. Escanaba (3.2%), and S. Dusseldorf (0.5%). All isolates were resistant to ceftiofur (100%), while most of them were resistant to ciprofloxacin (99.1%), amoxicillin-clavulanic acid (97.7%), trimethoprim-sulfamethoxazole (96.4%), ampicillin (92.3%), sulfisoxazole (92.2%), tetracyclines (90.4%), and nalidixic acid (90.4%), respectively. A single mutation of Ser83Phe (27.1%) and double mutations of Ser83Phe-Asp87Gly (25.9%) in GyrA were detected in 85 isolates, whereas mutations of Thr57Ser (63.9%) and Ser80Arg (36.1%) in ParC were detected in 122 isolates. qnrB, oqxAB, aac(6')-Ib, and qnrA were present in 50 (22.8%), 48 (21.9%), 26 (11.9%), and 1 (0.5%) isolate(s), respectively. Pulse field gel electrophoresis results revealed that those isolates recovered from the same type of PRTEM or the same sampling place shared identical or similar DNA profiles, antibiotic resistance phenotypes, and even plasmid-mediated quinolone resistance encoding genes. The findings indicate that Salmonella is commonly prevalent in PRTEMs at high concentrations in Shaanxi, China. More attention should be paid to the processing and storage of this ready-to-eat food to prevent bacterial contamination and foodborne outbreaks.

Increasing Frequencies of Antibiotic Resistant Non-typhoidal Salmonella Infections in Michigan and Risk Factors for Disease

Non-typhoidal Salmonella (NTS) are important enteric pathogens causing over 1 million foodborne illnesses in the U.S. annually. The widespread emergence of antibiotic resistance in NTS isolates has limited the availability of antibiotics that can be used for therapy. Since Michigan is not part of the FoodNet surveillance system, few studies have quantified antibiotic resistance frequencies and identified risk factors for NTS infections in the state. We obtained 198 clinical NTS isolates via active surveillance at four Michigan hospitals from 2011 to 2014 for classification of serovars and susceptibility to 24 antibiotics using broth microdilution. The 198 isolates belonged to 35 different serovars with Enteritidis (36.9%) predominating followed by Typhimurium (19.5%) and Newport (9.7%), though the proportion of each varied by year, residence, and season. The number of Enteritidis and Typhimurium cases was higher in the summer, while Enteritidis cases were significantly more common among urban vs. rural residents. A total of 30 (15.2%) NTS isolates were resistant to ≥1 antibiotic and 15 (7.5%) were resistant to ≥3 antimicrobial classes; a significantly greater proportion of Typhimurium isolates were resistant compared to Enteritidis isolates and an increasing trend in the frequency of tetracycline resistance and multidrug resistance was observed over the 4-year period. Resistant infections were associated with longer hospital stays as the mean stay was 5.9 days for patients with resistant isolates relative to 4.0 days for patients infected with susceptible isolates. Multinomial logistic regression indicated that infection with serovars other than Enteritidis [Odds ratio (OR): 3.8, 95% confidence interval (CI): 1.23-11.82] as well as infection during the fall (OR: 3.0; 95% CI: 1.22-7.60) were independently associated with resistance. Together, these findings demonstrate the importance of surveillance, monitoring resistance frequencies, and identifying risk factors that can aid in the development of new prevention strategies.

Prevalence of Multidrug Resistant Salmonellae with Increasing Frequency of Salmonella enterica Serovars Kentucky and Virchow among Hospitalized Diarrheal Cases in and around Delhi, India

Non-typhoidal salmonellae (NTS) are a major cause of acute diarrhea with characteristic multidrug resistance (MDR). In a hospital-based study, 81 NTS were isolated and tested for serotypes and antimicrobial resistance (AMR). Salmonella enterica isolates were classified into 7 different typable serovars, however, 19 (23%) isolates remained untypable. The most common serovars were S. Kentucky (48%), and S. Virchow (22%). Most of the NTS isolates displayed resistance to nalidixic acid (NA) (73%), ciprofloxacin (CIP) (48%), ampicillin (AM) and norfloxacin (NOR) (36% each), and gentamicin (CN) (31%). The AMR profiles for CN and NA; and AM, CIP, NA and NOR, were found to be high in S. Virchow (83%) and S. Kentucky (43%), respectively. Analysis of the pulsed-field gel electrophoresis patterns of S. Kentucky revealed 3 clusters. S. Kentucky has clones closely related to become prominent in recent years in Delhi. The AMR appears to be consistent with the change in MDR patterns during 2014-2017. The observed prevalence of S. Kentucky and S. Virchow in large numbers of diarrheal cases is novel. The NTS are mostly resistant to fluoroquinolones, which is the current drug of choice for treating diarrheal cases. MDR is very common among clonally related S. Kentucky.

A review of Salmonella enterica with particular focus on the pathogenicity and virulence factors, host specificity and antimicrobial resistance including multidrug resistance

Salmonella genus represents the most common foodborne pathogens frequently isolated from food-producing animals that is responsible for zoonotic infections in humans and animal species including birds. Thus, Salmonella infections represent a major concern to public health, animals, and food industry worldwide. Salmonella enterica represents the most pathogenic specie and includes > 2600 serovars characterized thus far. Salmonella can be transmitted to humans along the farm-to-fork continuum, commonly through contaminated foods of animal origin, namely poultry and poultry-related products (eggs), pork, fish etc. Some Salmonella serovars are restricted to one specific host commonly referred to as "host-restricted" whereas others have broad host spectrum known as "host-adapted" serovars. For Salmonella to colonize its hosts through invading, attaching, and bypassing the host's intestinal defense mechanisms such as the gastric acid, many virulence markers and determinants have been demonstrated to play crucial role in its pathogenesis; and these factors included flagella, capsule, plasmids, adhesion systems, and type 3 secretion systems encoded on the Salmonella pathogenicity island (SPI)-1 and SPI-2, and other SPIs. The epidemiologically important non-typhoidal Salmonella (NTS) serovars linked with a high burden of foodborne Salmonella outbreaks in humans worldwide included Typhimurium, Enteritidis, Heidelberg, and Newport. The increased number of NTS cases reported through surveillance in recent years from the United States, Europe and low- and middle-income countries of the world suggested that the control programs targeted at reducing the contamination of food animals along the food chain have largely not been successful. Furthermore, the emergence of several clones of Salmonella resistant to multiple antimicrobials worldwide underscores a significant food safety hazard. In this review, we discussed on the historical background, nomenclature and taxonomy, morphological features, physical and biochemical characteristics of NTS with a particular focus on the pathogenicity and virulence factors, host specificity, transmission, and antimicrobial resistance including multidrug resistance and its surveillance.

Increasing prevalence and dissemination of invasive nontyphoidal Salmonella serotype Typhimurium with multidrug resistance in hospitalized patients from southern Brazil

Introduction

Aim

Methods

Results

Conclusion

Occurrence, antimicrobial resistance and whole-genome sequencing analysis of Salmonella isolates from chicken carcasses imported into Iraq from four different countries

Salmonella is a major cause of human foodborne illnesses worldwide; however, little is known about its occurrence and genomic characteristics in food sources in many developing countries. This study investigates the occurrence, serotypes distribution, antimicrobial resistance, and multilocus sequence types (ST) of Salmonella isolated from 400 imported frozen chicken carcasses sold in the markets of Thi-Qar, south-eastern Iraq. Salmonella was detected in 46 out of 400 tested samples [11.5% (95% confidence interval: 8.5%-15.0%)]. S. Typhimurium was the most abundant (30.4%) among 14 different serotypes recovered from the tested frozen carcasses. Antimicrobial resistance was most frequently detected against tetracycline (84.4%), nalidixic acid (80.4%), streptomycin (69.6%) and trimethoprim/sulfamethoxazole (65.2%). Whole-genome sequencing (WGS) analysis revealed that 18 isolates harbored four β-lactamase resistance genes, with bla_CARB-2 was the most commonly (14/18) detected. It was possible to identify 8 multilocus sequence types from the WGS analysis of 40 out of the 46 Salmonella isolates; with ST-11 (among S. Enteritidis) and ST-19 (among S. Typhimurium) were the most frequently detected. These results add to our understanding of the global epidemiology of Salmonella. Our work stands as one of the first reports on WGS analysis of Salmonella from retail chicken in a Middle-Eastern country. Results from this study could be valuable for guiding an informed import risk analysis aiming at reducing the exposure risk from Salmonella through imported chicken carcasses into Iraq. This work demonstrates the value of WGS as a promising tool for supporting evidence-based food safety hazard characterization.

Emerging mechanisms of antimicrobial resistance in bacteria and fungi: advances in the era of genomics

Bacteria and fungi continue to develop new ways to adapt and survive the lethal or biostatic effects of antimicrobials through myriad mechanisms. Novel antibiotic resistance genes such as lsa(C), erm(44), VCC-1, mcr-1, mcr-2, mcr-3, mcr-4, bla _KLUC-3 and bla _KLUC-4 were discovered through comparative genomics and further functional studies. As well, mutations in genes that hitherto were unknown to confer resistance to antimicrobials, such as trm, PP2C, rpsJ, HSC82, FKS2 and Rv2887, were shown by genomics and transcomplementation assays to mediate antimicrobial resistance in Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecium, Saccharomyces cerevisae, Candida glabrata and Mycobacterium tuberculosis, respectively. Thus, genomics, transcriptomics and metagenomics, coupled with functional studies are the future of antimicrobial resistance research and novel drug discovery or design.

Phenotypic and Molecular Characterization of Salmonella Enteritidis SE86 Isolated from Poultry and Salmonellosis Outbreaks

Salmonella Enteritidis remains a standout among the leading causes of foodborne diseases worldwide. Previous studies have demonstrated that a unique clonal group of Salmonella Enteritidis, named SE86, is involved in foodborne outbreaks in southern Brazil and is frequently identified among strains isolated from poultry. The aim of this study was to determine the influence of the isolation source (food products involved in salmonellosis outbreaks and poultry sources) on the phenotypic and molecular characteristics of Salmonella Enteritidis SE86. A biofilm formation assay, antimicrobial susceptibility test, polymerase chain reaction identification of virulence-associated genes, and phage type 4 (PT4) assessment were performed to characterize Salmonella Enteritidis SE86. The human strains presented less antimicrobial resistance than the poultry strains. Resistance to some substances was related to the isolation source of the strain. Strains of the same clonal group presented different biofilm production abilities. Biofilm formation was independent of the isolation source at all temperatures. Temperature influenced biofilm formation only by the poultry strains. Most of the investigated genes presented a high frequency and a regular distribution, regardless of the isolation source. The spvB, spiA, pagC, sipB, prgH, spaN, sitC, and lpfC genes were associated with the avian strains, whereas iroN was associated with the strains isolated from food products involved in salmonellosis outbreaks. Most strains belonged to PT4. No relationship was found between biofilm production and antimicrobial resistance or between the virulence profile and biofilm production or antimicrobial resistance.

Importance of Wild Species Kept in Captivity as Reservoirs of Salmonella Serotypes for Human in Petting Exhibitions and Zoo in Iran with Focus on Antimicrobial Resistance

Salmonella spp. is the leading cause of zoonotic enteric diseases wich represents a public health concern worldwide. The incidence of zoo-associated salmonellosis is rather high due to the high prevalence and shedding of this bacterium from wild animals specially kept in stressful conditions. To determine the potential public health risk presented by zoo animals in Semnan, we investigated the prevalence of Salmonella serovars Enteritidis and Typhimurium among wild animal species kept in the zoo and pet shops. Totally, 152 fecal samples from species in the zoo and pet shops were collected and Salmonella prevalence and identification was assessed via standard bacteriologic culture methods, serotyping, multiplex-PCR and antimicrobial susceptibility testing. Overall, 21% (32/152) of the samples were confirmed positive for Salmonella and serotyping showed 12.5% (19/32) Salmonella serovar Enteritidis and 8.5% (13/32) serovar Typhimurium, respectively. All the Salmonella isolates were sensitive to Chloramphenicole, Flurefenicole, Meropenem, Ceftizoxime, Imipenem and Ampicillin, while resistance was observed in the case of Nalidixic acid (78%) as the highest resistance, Streptomycin (28%), Oxytetracycline, Neomycin, Furazolidone (each one 15%) and Lincospectin (9.3%). The high occurrence of multidrug resistance Salmonella in zoo and pet animals represents a potential threat to public health and requires strict surveillance and application of hygienic criteria.