Characterization of antimicrobial resistance in Salmonella enterica strains isolated from Brazilian poultry production

A multidisciplinary approach to analyze the antimicrobial resistance in natural ecosystems

Antimicrobial Resistance (AMR) poses a global threat to both human health and environmental well-being. Our study delved into Costa Rican wildlife reserves, uncovering a substantial human impact on these ecosystems and underscoring the imperative to pinpoint AMR hotspots. Embracing a One Health perspective, we advocated for a comprehensive landscape analysis that intricately intertwined geographic, climatic, forest, and human factors. This study illuminated the link between laboratory results and observed patterns of antimicrobial use, thereby paving the way for sustainable solutions. Our innovative methodology involved deploying open-ended questions to explore antimicrobial usage across livestock activities, contributing to establishing a comprehensive methodology. Non-invasive sampling in wildlife emerged as a critical aspect, shedding light on areas contaminated by AMR. Feline species, positioned at the apex of the food chain, acted as sentinels for environmental health due to heightened exposure to improperly disposed waste. Regarding laboratory findings, each sample revealed the presence of at least one antimicrobial resistance gene (ARG). Notably, genes encoding resistance to tetracyclines dominated (94.9%), followed by beta-lactams (75.6%), sulfonamides (53.8%), aminoglycosides (51.3%), quinolones (44.9%), phenicols (25.6%), and macrolides (20.5%). Genes encoding polymyxins were not detected. Moreover, 66% of samples carried a multi-resistant microbiome, with 15% exhibiting resistance to three antimicrobial families and 51% to four. The absence of a correlation between forest coverage and ARG presence underscored the profound human impact on wildlife reserves, surpassing previous estimations. This environmental pressure could potentially modify microbiomes and resistomes in unknown ways. As not all antimicrobial families encoding ARGs were utilized by farmers, our next step involved evaluating other human activities to identify the primary sources of contamination. This comprehensive study contributed crucial insights into the intricate dynamics of AMR in natural ecosystems, paving the way for targeted interventions and sustainable coexistence.

Occurrence, virulence, and resistance genes in Salmonella enterica isolated from an integrated poultry company in Jordan

Salmonella is considered one of the most common foodborne pathogens worldwide. The annual number of hospitalizations and deaths related to zoonotic salmonellosis, which is transmitted from animals to humans and infects poultry and meat, is expected to be significant. Hence, the primary aims of this research were to isolate and characterize Salmonella species obtained from an integrated poultry company and identify some virulence, and antimicrobial resistance, with a specific concern about colistin resistance genes. A total of 635 samples collected from various sources in an integrated company in Jordan were screened for Salmonella species accompanying their virulence and antimicrobial resistance genes. Samples were collected from parent stock house drag swabs, broiler farms, premix, cecum at the slaughterhouse level, prechilling and postchilling stages, and the final product. Salmonella species were detected in 3% (6/200) of investigated parent stock house drag swabs, 13.8% (11/80) from cloacal swabs from broiler farms, 16.9% (11/65) from boiler farms premix, 24.4% (11/45) from the cecum at slaughterhouse level, 16.4% (9/55) from the prechilling stage, 37.8% (17/45) from the postchilling stage and 53.3% (24/45) from the final product stage. No isolates were detected in feed mills (0/20), parents' premix (0/40), or hatcheries (0/40). Salmonella isolates were resistant to ciprofloxacin (91.0%), nalidixic acid (86.5%), doxycycline (83.1%), tetracycline (83.1%), sulphamethoxazole-trimethoprim (79.8%) and ampicillin (76.4%). Serotyping shows that S. Infantis was the predominant serovar, with 56.2%. Based on the minimum inhibitory concentration (MIC) test, 39.3% (35/89) of the isolates were resistant to colistin; however, no mcr genes were detected. Among antimicrobial-resistant genes, blaTEM was the most prevalent (88.8%). Furthermore, the spvC, ompA, and ompF virulence genes showed the highest percentages (97.8%, 97.8%, and 96.6%, respectively). In conclusion, Salmonella isolates were found at various stages in the integrated company. S. Infantis was the most prevalent serotype. No mcr genes were detected. Cross-contamination between poultry production stages highlights the importance of good hygiene practices. Furthermore, the presence of virulence genes and the patterns of antimicrobial resistance present significant challenges for public health.

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.

Association between antimicrobial resistance and biofilm forming ability of Salmonella enterica serotypes from commercial broiler farms in Brazil

1. This study determined the antimicrobial resistance profile and the biofilm-forming ability of Salmonella enterica strains isolated from commercial broiler houses over a three-year period in southern Brazil.

2. Of the 720 drag swabs analysed, 37 (5.1%) tested positive for non-typhoidal Salmonella spp. and S. Heidelberg was the most frequent serovar.

3. Among the antimicrobial resistant strains (83.8%; 31/37), resistance was most common to tetracycline, ampicillin and nalidixic acid. Multidrug resistance was found in 65% (24/37) of the isolates, with a large proportion of multidrug resistant S. Heidelberg strains (81%; 13/16).

4. In total, 65% (24/37) of the isolates showed the ability to produce biofilm and multiple antimicrobial resistance was negatively correlated with biofilm formation.

5. Strains susceptible to all tested antimicrobials tended to form stronger biofilms than multidrug resistant ones. This suggested that Salmonella spp. with less antimicrobial resistance depend more on the protection provided by biofilm to survive in the farm environment.

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

Simple Summary

Salmonellosis is a human and animal disease caused by Salmonella, a bacterial genus classified into different species, subspecies, and serological variants (serovars) according to adaptation to one or more different hosts (animals and humans), pathogenicity profiles, and antigenic properties. Some specific Salmonella serovars can spread more easily in the enteric microbiota of avian species, often causing disease in birds and/or being transmitted to humans through food (such as chicken and eggs). Antimicrobial resistance (AMR) has also been reported in poultry-associated Salmonella isolates due to the widespread use of antimicrobials on farms. The availability of comprehensive data on the emergence and spread of Salmonella serovars, as well as their AMR profiles in farms and food products in Brazil (a major producer of poultry in the World), is necessary to understand their relevance in all avian production chains and also occurrence in poultry-derived foods. This article aims to provide an overview of the genus Salmonella and the main serovars that emerged in Brazilian poultry over time (Gallinarum, Typhimurium, Enteritidis, Heidelberg, and Minnesota), reviewing the scientific literature and suggesting more effective prevention and control for the future.

Abstract

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.

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.

Antimicrobial Resistance in Rural Settings in Latin America: A Scoping Review with a One Health Lens

Antimicrobial resistance (AMR) in rural Latin America is not fully understood. The transmission pathways are partially known since research predominantly focuses on the urban hospital setting. The contribution to AMR from environmental factors is usually only mentioned in large-scale animal production. To understand the state of the literature on AMR in rural LA, we carried out a scoping review using the One Health (OH) perspective. OH recognises the concomitant contributions and interconnectedness of humans, animal, and the environment, thus, we used the OH perspective to select those articles adopting a holistic view of the problem. We searched original articles in English, Spanish, and Portuguese in four peer-reviewed databases and included 21 publications in the analysis. We charted data on bibliometrics, design, data collection sources, and instruments. We identified the human, animal, and environmental contributions to AMR in rural locations, and information gaps on AMR transmission routes and AMR drivers. Intensive and non-intensive animal production systems and agricultural practices were the most frequently found human contributions to AMR. Poultry, swine, cattle, and fish were the most frequent livestock mentioned as sources of AMR bacteria. Animal carriage and/or transfer of AMR determinants or bacteria was recognised as the primary contribution of livestock to the problem, while water, soil, and farming were predominant environmental contributions. We found that only 1 article out of 21 considered the OH approach as a framework for their sampling scheme, whereas 5 out 21 discussed all the three OH components. There were hardly any descriptions of humans or human waste as reservoirs for AMR in rural locations, and rural health centres or hospitals and wildlife were not represented. No studies identified mining as an anthropogenic activity driving AMR. More OH-oriented studies, with emphasis on molecular approaches—for identification and comparison of AMR genes—are sorely needed to understand better the existence of a network of interconnected transmission routes in rural Latin America and provide efficient strategies to prevent further AMR emergence.

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

Salmonella enterica serovars are associated with numerous annual deaths worldwide and are responsible for a large number of foodborne diseases. Within this frame of reference, knowledge of antimicrobial susceptibility represents the fundamental approach of most Salmonella treatments. Therefore, scientific publications of antimicrobial susceptibilities and resistance must be precise, with interpretations adjusted to a particular standard. Hence, the three objectives in this study were: (i) to describe the frequency of antimicrobial-resistant isolates of Non-Typhoidal Salmonella (NTS) isolated from beef, pork, chicken meat, and other meat products; (ii) to describe the distribution of serovars and their multi-resistance to antibiotics for clinical use (veterinary and human) between 1996 and 2019; and (iii) to propose additional considerations that could improve the use and usefulness of the published results. Our results determined that the predominant isolates came from poultry. Enteritidis and Typhimurium were the most reported serovars by MIC (with both having the highest resistance to TET) while the lowest resistance was to CIP and CRO for Enteritidis and Typhimurium, respectively. The multi-resistance pattern AMP AMC CEP GEN KAN STR TET was the most frequently observed pattern by MIC in Montevideo and Seftenberg, while, for disc diffusion, the pattern AMP STR TET was the most frequent in the Bredeney serotype. In conclusion, researchers should carry out homogeneous sampling procedures, identify the types of the samples, use standard identification methods, and employ appropriate standards for antimicrobial susceptibility interpretation. Additionally, there is also a need for all WHO members to comply with the WHA 73.5 resolution. Our final recommendation is for all producers to reduce antibiotic prophylactic use.

Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands

Salmonella Infantis, a common contaminant of poultry products, is known to harbor mobile genetic elements that confer multi-drug resistance (MDR) and have been detected in many continents. Here, we report four MDR S. Infantis strains recovered from poultry house environments in Santa Cruz Island of the Galapagos showing extended-spectrum β-lactamase (ESBL) resistance and reduced fluoroquinolone susceptibility. Whole-genome sequencing (WGS) revealed the presence of the ESBL-conferring bla_CTX-M-65 gene in an IncFIB-like plasmid in three S. Infantis isolates. Multi-locus sequence typing (MLST) and single nucleotide variant/polymorphism (SNP) SNVPhyl analysis showed that the S. Infantis isolates belong to sequence type ST32, likely share a common ancestor, and are closely related (1–3 SNP difference) to bla_CTX-M-65-containing clinical and veterinary S. Infantis isolates from the United States and Latin America. Furthermore, phylogenetic analysis of SNPs following core-genome alignment (i.e., ParSNP) inferred close relatedness between the S. Infantis isolates from Galapagos and the United States. Prophage typing confirmed the close relationship among the Galapagos S. Infantis and was useful in distinguishing them from the United States isolates. This is the first report of MDR bla_CTX-M-65-containing S. Infantis in the Galapagos Islands and highlights the need for increased monitoring and surveillance programs to determine prevalence, sources, and reservoirs of MDR pathogens.

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.

Antimicrobial resistance genes in bacteria from animal-based foods

Antimicrobial resistance is a worldwide public health threat. Farm animals are important sources of bacteria containing antimicrobial resistance genes (ARGs). Although the use of antimicrobials in aquaculture and livestock has been reduced in several countries, these compounds are still routinely applied in animal production, and contribute to ARGs emergence and spread among bacteria. ARGs are transmitted to humans mainly through the consumption of products of animal origin (PAO). Bacteria can present intrinsic resistance, and once antimicrobials are administered, this resistance may be selected and multiply. The exchange of genetic material is another mechanism used by bacteria to acquire resistance. Some of the main ARGs found in bacteria present in PAO are the bla, mcr-1, cfr and tet genes, which are directly associated to antibiotic resistance in the human clinic.

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.

Genetic Characterization of Antimicrobial-Resistant Escherichia coli Isolated from a Mixed-Use Watershed in Northeast Georgia, USA

In order to determine the role of surface water in the development and spread of antibiotic-resistant (AR) bacteria, water samples were collected quarterly from 2015 to 2016 from a mixed-use watershed in Georgia. In our previous study, 496 Escherichia coli were isolated from surface water, out of which, 34 isolates were resistant to antimicrobials. For the current study, these 34 AR E. coli were characterized using pulsed-field gel electrophoresis, AR gene detection, plasmid replicon typing, class I integron detection, and multi-locus sequence typing. Genes were identified as conferring resistance to azithromycin (mph(A)); β-lactams (bla_CMY, bla_CTX, bla_TEM); chloramphenicol (floR); streptomycin (strA, strB); sulfisoxazole (sul1, sul2); tetracycline (tetA, tetB, tetC); and trimethoprim/sulfamethoxazole (dhfr5, dhfr12). Five ciprofloxacin- and/or nalidixic-resistant isolates contained point mutations in gyrA and/or parC. Most of the isolates (n = 28) carried plasmids and three were positive for class I integrons. Twenty-nine sequence types (ST) were detected, including three epidemic urinary-tract-infection-associated ST131 isolates. One of the ST131 E. coli isolates exhibited an extended-spectrum β-lactamase (ESBL) phenotype and carried bla_CTX-M-15 and bla_TEM-1. To our knowledge, this is the first study on the emergence of an ESBL-producing E. coli ST131 from environmental water in the USA, which poses a potential risk to human health through the recreational, agricultural, or municipal use of this natural resource. This study identified E. coli with AR mechanisms to commonly used antimicrobials and carrying mobile genetic elements, which could transfer AR genes to other bacteria in the aquatic environment.

Fecal Colonization of Extended-Spectrum Beta Lactamase-Producing Salmonella spp. in Broilers in Lorestan Province of Iran

Background: Poultry is considered as a major source of human contamination with nontyphoidal Salmonella species. Global concern regarding the emergence and dispersion of extended-spectrum beta-lactamase (ESBLs)-producing isolates in broilers has increased during recent years. Objective: This study was proposed to evaluate the prevalence of Salmonella and the associated ESBLs in broilers in Lorestan province of Iran. Materials and Methods: Five hundred fresh fecal samples of broilers were phenotypically screened for Salmonella. The isolates were confirmed molecularly using an invA-based polymerase chain reaction (PCR). Confirmatory combination disk method was applied for phenotypic detection of ESBLs among the isolates, followed by molecular identification of blaCTX-M, blaTEM, and blaSHV genes in 3 single PCR assays among positive isolates. Chi-square test in SPSS software was used for the assessment of statistical relationships. Results: Of the 95 Salmonella isolates detected using routine bacteriological methods, all were confirmed molecularly. They generated the expected 254-bp amplicon. Moreover, 13 isolates were phenotypically recognized as ESBL determinants, among which 9 and 4 harbored blaCTX-M and blaTEM, respectively. No blaSHV and co-existence of the genes were determined. Conclusion: The threat imposed by dissemination of ESBL-producing non-typhoidal Salmonella spp. isolated from broilers was confirmed in the studied region. Continuous monitoring programs, application of biosecurity measures, and prudent prescription of antibiotics are warranted in order to prevent the introduction or dispersion of the ESBL-producing Salmonella.

Detection and characterization of multidrug-resistant Salmonella enterica serovar Infantis as an emerging threat in poultry farms of Faisalabad, Pakistan

AIMS

The aim of this study was the molecular identification of Salmonella enterica serovar Infantis (S. Infantis) isolated from poultry samples and their antimicrobial resistance and virulence profiling.

METHODS AND RESULTS

A total of 149 isolates, belonging to genus Salmonella, originally isolated from 340 suspected poultry post mortem specimens reported by us earlier were preliminary identified as Salmonella by biochemical methods and confirmed by polymerase chain reaction targeting genus-specific gene invA. Targeting serovar-specific gene fragment (fljB) resulted in confirmation of 54 isolates as S. Infantis which were further confirmed by sequencing of 16S RNA and fljB genes. Swimming and swarming motilities were detected in 98·1 and 11·1% isolates respectively. Phenotypic disc diffusion assay against 23 antimicrobial agents showed the highest resistance against pefloxacin (PEF) (94·4%), chloramphenicol (83·3%) and imipenem (77·7%) while 5·3% isolates showed extended-spectrum β-lactamase production. Fifty-nine genes reported for antimicrobial resistance and 12 for conferring virulence were targeted. The most prevalent resistance gene for aminoglycosides was aadA (42·3%), for quinolone resistance determining region parE (62·5%), for penicillin's Int1 (62·9%), for chloramphenicol cat3 (66·1%) and for beta-lactams bla_{TEM -1} (44·4%). Among efflux pump coding genes, armA showed highest (74·2%) prevalence and for virulence, a high prevalence of SopE (89·2%) showed the zoonotic potential of the isolates. The activity of efflux pumps was detected through Ethidium Bromide-agar method.

CONCLUSIONS

Poultry could act as reservoirs of multidrug resistance Salmonella.

SIGNIFICANCE AND IMPACT OF THE STUDY

We firstly report the prevalence and molecular characterization of virulence/drug resistance in S. Infantis from this region and the results may contribute to designing precisely targeted therapy. This study has also highlighted the possible emergence of S. Infantis with zoonotic potential.

Transmission routes of ESBL/pAmpC producing bacteria in the broiler production pyramid, a literature review

Plasmid mediated Extended Spectrum Beta-Lactamase and AmpC Beta-Lactamase (ESBL/pAmpC) producing bacteria are resistant to beta-lactam antimicrobials and are widespread in humans, the environment and animals. Animals, especially broilers, are an important reservoir of ESBL/pAmpC producing bacteria. To control ESBL/pAmpC prevalence in broilers, transmission within the entire broiler production pyramid should be considered. This study, including 103 articles originating from two electronic databases, searched for evidence for possible routes of transmission of ESBL/pAmpC producing bacteria in the broiler production pyramid. Possible routes of transmission were categorised as 1) vertical between generations, 2) at hatcheries, 3) horizontal on farm, and 4) horizontal between farms and via the environment of farms. This review presents indications for transmission of ESBL/pAmpC producing bacteria for each of these routes. However, the lack of quantitative results in the literature did not allow an estimation of the relative contribution or magnitude of the different routes. Future research should be specifically targeted towards such information as it is crucial to guide reduction strategies for the spread of ESBL/pAmpC producing bacteria in the broiler production chain.

Distribution and dissemination of antimicrobial-resistant Salmonella in broiler farms with or without enrofloxacin use

BACKGROUND

Salmonella is a major zoonotic food-borne pathogen that persists on poultry farms, and animals undergo reinfection with endemic strains. The present study aimed to investigate the characteristics and dissemination of antimicrobial-resistant Salmonella within and between broiler farms that used enrofloxacin and those that did not.

RESULTS

Cloacal and environmental (litter, feed, and water) samples from two selected flocks in each of 12 farms owned by the same company were collected three times over a 30-day period of two production cycles during 2015-2016. The rate of Salmonella isolation was 7.8% (123/1584). Nine Salmonella serotypes (116 isolates) and seven untypable isolates were identified, and Salmonella Montevideo was the most prevalent serotype. Azithromycin-resistant (17.9%) and colistin-resistant (3.3%) isolates were detected, and multidrug-resistant isolates (43.1%) were also observed. No isolate was resistant to enrofloxacin or ciprofloxacin; however, intermediate resistance to enrofloxacin was significantly higher (P < 0.05) in farms that used enrofloxacin than in those that did not. The rate of multi-drug resistance among litter isolates (25/44, 56.8%) was significantly higher (P < 0.05) than that among cloacal swab (24/67, 35.8%) and feed (4/12, 33.3%) isolates. Pulsed-field gel electrophoresis (PFGE) analysis of strains of the same serotype was conducted to determine their epidemiological relationship. The PFGE types were classified into 31 groups with a 100% correlation cutoff in dendrograms for Salmonella Montevideo isolates, which showed 100% genomic identity based on age, sample type, flock, and production cycle within and between farms.

CONCLUSION

The present study highlights the occurrence of horizontal transmission and cyclic contamination with antimicrobial-resistant Salmonella in broiler farms owned by the same company. Litter may be a good indicator of indoor environmental contamination with antimicrobial-resistant Salmonella on farms. Additionally, enrofloxacin use may be one of the factors promoting resistance towards it in Salmonella.

Salmonella Gallinarum field isolates and its relationship to vaccine strain SG9R

1. The aim of the present study was to determine if the 9R-strain of the Salmonella Gallinarum live vaccine was responsible for having fowl typhoid outbreaks in chicken flocks from both chicken and turkey breeders as well as to verify the antimicrobial resistance of the isolates from the outbreaks. 2. The triplex polymerase chain reaction, standard antimicrobial test, beta-lactamase genes identification and Ion Torrent PMG whole-genome sequence were used in the field isolates and in the vaccine strain of S. Gallinarum. 3. The 60 tested isolates were not from vaccine origin and manifested high resistance to drugs from macrolide and quinolone groups. Whole-genome sequencing (WGS) and single nucleotide polymorphism analysis on selected isolates for core genes from Salmonella enterica confirmed the wild origin of these isolates and showed two possible sources of S. Gallinarum in the studied outbreaks. 4. S. Gallinarum isolated from fowl typhoid outbreaks in the studied period were not caused by the use of the SG9R live vaccine. The source of strains sequenced was diverse.

Horizontal Dissemination of Antimicrobial Resistance Determinants in Multiple Salmonella Serotypes following Isolation from the Commercial Swine Operation Environment after Manure Application

The aim of this study was to characterize the plasmids carrying antimicrobial resistance (AMR) determinants in multiple Salmonella serotypes recovered from the commercial swine farm environment after manure application on land. Manure and soil samples were collected on day 0 before and after manure application on six farms in North Carolina, and sequential soil samples were recollected on days 7, 14, and 21 from the same plots. All environmental samples were processed for Salmonella, and their plasmid contents were further characterized. A total of 14 isolates including Salmonella enterica serotypes Johannesburg (n = 2), Ohio (n = 2), Rissen (n = 1), Typhimurium var5- (n = 5), Worthington (n = 3), and 4,12:i:- (n = 1), representing different farms, were selected for plasmid analysis. Antimicrobial susceptibility testing was done by broth microdilution against a panel of 14 antimicrobials on the 14 confirmed transconjugants after conjugation assays. The plasmids were isolated by modified alkaline lysis, and PCRs were performed on purified plasmid DNA to identify the AMR determinants and the plasmid replicon types. The plasmids were sequenced for further analysis and to compare profiles and create phylogenetic trees. A class 1 integron with an ANT(2″)-Ia-aadA2 cassette was detected in the 50-kb IncN plasmids identified in S Worthington isolates. We identified 100-kb and 90-kb IncI1 plasmids in S Johannesburg and S Rissen isolates carrying the bla_CMY-2 and tet(A) genes, respectively. An identical 95-kb IncF plasmid was widely disseminated among the different serotypes and across different farms. Our study provides evidence on the importance of horizontal dissemination of resistance determinants through plasmids of multiple Salmonella serotypes distributed across commercial swine farms after manure application.IMPORTANCE The horizontal gene transfer of antimicrobial resistance (AMR) determinants located on plasmids is considered to be the main reason for the rapid proliferation and spread of drug resistance. The deposition of manure generated in swine production systems into the environment is identified as a potential source of AMR dissemination. In this study, AMR gene-carrying plasmids were detected in multiple Salmonella serotypes across different commercial swine farms in North Carolina. The plasmid profiles were characterized based on Salmonella serotype donors and incompatibility (Inc) groups. We found that different Inc plasmids showed evidence of AMR gene transfer in multiple Salmonella serotypes. We detected an identical 95-kb plasmid that was widely distributed across swine farms in North Carolina. These conjugable resistance plasmids were able to persist on land after swine manure application. Our study provides strong evidence of AMR determinant dissemination present in plasmids of multiple Salmonella serotypes in the environment after manure application.

Diversity of plasmids harboring blaCMY-2 in multidrug-resistant Escherichia coli isolated from poultry in Brazil

Multidrug-resistance (MDR) has been increasingly reported in Gram-negative bacteria from the intestinal microbiota, environment and food-producing animals. Resistance plasmids able to harbor different transposable elements are capable to mobilize antimicrobial resistance genes and transfer to other bacterial hosts. Plasmids carrying bla_CMY are frequently associated with MDR. The present study assessed the presence of plasmid-encoded ampC genes (bla_cmy, bla_mox, bla_fox, bla_lat, bla_act, bla_mir, bla_dha, bla_mor) in commensal E. coli isolated from apparently healthy broiler chickens. Furthermore, we characterized the plasmids and identified those harboring the resistance genes. We isolated 144/200 (72%) of E. coli isolates with resistance to cefotaxime and the resistance gene identified was bla_CMY-2. The pulsed-field gel electrophoresis (PFGE) analysis showed high diversity of the genetic profiles. The phylogenetic groups A, B1, B2, and D were identified among E. coli isolates and group D was the most prevalent. The PCR-based replicon typing (PBRT) analysis identified four distinct plasmid incompatibility groups (Inc) in MDR isolates. Moreover, plasmids harboring bla_CMY-2, ranged in size from 50kb to 150kb and 51/144 (35%) belonged to IncK, 21/144 (14.5%) to IncB/O, 8/144 (5.5%) to IncA/C, 1/144 (0.5%) to IncI, while 63/144 (44.5%) were not typeable by PBRT. Overall, a high prevalence of bla_CMY-2 genes was found in a diverse population of commensal MDR E. coli from poultry in Brazil, harbored into different plasmids.

Prevalence and Diversity of Salmonella Serotypes in Ecuadorian Broilers at Slaughter Age

Salmonella is frequently found in poultry and represent an important source for human gastrointestinal infections worldwide. The aim of this study was to investigate the prevalence, genotypes and antimicrobial resistance of Salmonella serotypes in broilers from Ecuador. Caeca content from 388 at random selected broiler batches were collected in 6 slaughterhouses during 1 year and analyzed by the ISO 6579/Amd1 protocol for the isolation for Salmonella. Isolates were serotyped and genotypic variation was acceded by pulsed field gel electrophoresis. MIC values for sulfamethoxazole, gentamicin, ciprofloxacin, ampicillin, cefotaxime, ceftazidime, tetracycline, streptomycin, trimethropim, chloramphenicol, colistin, florfenicol, kanamycin and nalidixic acid were obtained. Presence of blaCTX-M, blaTEM, blaSHV and blaCMY; and mcr-1 plasmid genes was investigated in resistant strains to cefotaxime and colistin respectively. Prevalence at batch level was 16.0%. The most common serotype was S. Infantis (83.9%) followed by S. Enteritidis (14.5%) and S. Corvallis (1.6%). The pulsed field gel electrophoresis analysis showed that S. Corvallis, S. Enteritidis and S. Infantis isolates belonged to 1, 2 and 12 genotypes respectively. S. Infantis isolates showed high resistance rates to 12 antibiotics ranging from 57.7% (kanamycin) up to 98.1% (nalidixic acid and sulfamethoxazole). All S. Enteritidis isolates showed resistance to colistin. High multiresistant patterns were found for all the serotypes. The blaCTX-M gene was present in 33 S. Infantis isolates while mcr-1 was negative in 10 colistin resistant isolates. This study provides the first set of scientific data on prevalence and multidrug-resistant Salmonella coming from commercial poultry in Ecuador.

Genomic Microbial Epidemiology Is Needed to Comprehend the Global Problem of Antibiotic Resistance and to Improve Pathogen Diagnosis

Contamination of waste effluent from hospitals and intensive food animal production with antimicrobial residues is an immense global problem. Antimicrobial residues exert selection pressures that influence the acquisition of antimicrobial resistance and virulence genes in diverse microbial populations. Despite these concerns there is only a limited understanding of how antimicrobial residues contribute to the global problem of antimicrobial resistance. Furthermore, rapid detection of emerging bacterial pathogens and strains with resistance to more than one antibiotic class remains a challenge. A comprehensive, sequence-based genomic epidemiological surveillance model that captures essential microbial metadata is needed, both to improve surveillance for antimicrobial resistance and to monitor pathogen evolution. Escherichia coli is an important pathogen causing both intestinal [intestinal pathogenic E. coli (IPEC)] and extraintestinal [extraintestinal pathogenic E. coli (ExPEC)] disease in humans and food animals. ExPEC are the most frequently isolated Gram negative pathogen affecting human health, linked to food production practices and are often resistant to multiple antibiotics. Cattle are a known reservoir of IPEC but they are not recognized as a source of ExPEC that impact human or animal health. In contrast, poultry are a recognized source of multiple antibiotic resistant ExPEC, while swine have received comparatively less attention in this regard. Here, we review what is known about ExPEC in swine and how pig production contributes to the problem of antibiotic resistance.