Antimicrobial resistance and virulence genes in Salmonella enterica isolates from dairy cows

Serovars, Virulence and Antimicrobial Resistance Genes of Non-Typhoidal Salmonella Strains from Dairy Systems in Mexico

Salmonella isolated from dairy farms has a significant effect on animal health and productivity. Different serogroups of Salmonella affect both human and bovine cattle causing illness in both reservoirs. Dairy cows and calves can be silent Salmonella shedders, increasing the possibility of dispensing Salmonella within the farm. The aim of this study was to determine the genomic characteristics of Salmonella isolates from dairy farms and to detect the presence of virulence and antimicrobial resistance genes. A total of 377 samples were collected in a cross-sectional study from calves, periparturient cow feces, and maternity beds in 55 dairy farms from the states of Aguascalientes, Baja California, Chihuahua, Coahuila, Durango, Mexico, Guanajuato, Hidalgo, Jalisco, Queretaro, San Luis Potosi, Tlaxcala, and Zacatecas. Twenty Salmonella isolates were selected as representative strains for whole genome sequencing. The serological classification of the strains was able to assign groups to only 12 isolates, but with only 5 of those being consistent with the genomic serotyping. The most prevalent serovar was Salmonella Montevideo followed by Salmonella Meleagridis. All isolates presented the chromosomal aac(6')-Iaa gene that confers resistance to aminoglycosides. The antibiotic resistance genes qnrB19, qnrA1, sul2, aph(6)-Id, aph(3)-ld, dfrA1, tetA, tetC, flor2, sul1_15, mph(A), aadA2, blaCARB, and qacE were identified. Ten pathogenicity islands were identified, and the most prevalent plasmid was Col(pHAD28). The main source of Salmonella enterica is the maternity areas, where periparturient shedders are contaminants and perpetuate the pathogen within the dairy in manure, sand, and concrete surfaces. This study demonstrated the necessity of implementing One Health control actions to diminish the prevalence of antimicrobial resistant and virulent pathogens including Salmonella.

Synthesizing the connections between environmental disturbances and zoonotic spillover

Zoonotic spillover is a phenomenon characterized by the transfer of pathogens between different animal species. Most human emerging infectious diseases originate from non-human animals, and human-related environmental disturbances are the driving forces of the emergence of new human pathogens. Synthesizing the sequence of basic events involved in the emergence of new human pathogens is important for guiding the understanding, identification, and description of key aspects of human activities that can be changed to prevent new outbreaks, epidemics, and pandemics. This review synthesizes the connections between environmental disturbances and increased risk of spillover events based on the One Health perspective. Anthropogenic disturbances in the environment (e.g., deforestation, habitat fragmentation, biodiversity loss, wildlife exploitation) lead to changes in ecological niches, reduction of the dilution effect, increased contact between humans and other animals, changes in the incidence and load of pathogens in animal populations, and alterations in the abiotic factors of landscapes. These phenomena can increase the risk of spillover events and, potentially, facilitate new infectious disease outbreaks. Using Brazil as a study model, this review brings a discussion concerning anthropogenic activities in the Amazon region and their potential impacts on spillover risk and spread of emerging diseases in this region.

Prevalence and molecular characterization of foodborne and human-derived Salmonella strains for resistance to critically important antibiotics

The primary goals of this cross-sectional study were to screen various food/water, and human samples for the presence of Salmonella species, and to assess the phenotypic and genetic relationship between resistances found in food and human Salmonella isolates to critically important antibiotics. Between November 2019 and May 2021, 501 samples were randomly collected for Salmonella isolation and identification using standard culturing methods, biochemical, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and PCR techniques. Antimicrobial susceptibility testing was performed on confirmed Salmonella species, and PCR was used to investigate the genetic components that confer these resistance traits. Salmonella enterica subspecies enterica was confirmed in 35 (6.99%) of the samples (raw food = 23, ready-to-eat food/drink (REF/D) = 5, human = 7). Seventeen of them were antibiotic-resistant to at least one class, and eight were multidrug-resistant (MDR) isolates (raw food = 7, human = 1). All Salmonella isolates were susceptible to carbapenems, third and fourth-generation cephalosporins, and monobactam antibiotics. Resistance phenotypes to aminoglycosides (48.57%), β-lactams (20%), and tetracycline (17.14%), as well as associated genes such as aadA, bla_TEM , bla_Z , and tetA, as well as dfrA and sul1, were prevalent in Salmonella isolates. Colistin resistance genotype (mcr1) was detected in three (8.57 %) isolates recovered from egg, cattle mince, and rabbit meat, and the total incidence was 14.29 % when two isolates exhibited resistance phenotypes were considered. Furthermore, four (11.43%) MDR isolates shared the bla_TEM and bla_Z genes, and one (2.86%) isolate contained three extended spectrum β-lactams producing genes (ESBL), namely bla_CTX , bla_TEM , and bla_Z . The gyrA gene was expressed by one of three foodborne Salmonella isolates (8.57%) with ciprofloxacin resistance phenotypes. To the best of our knowledge, this is the first report from Egypt identifying colistin resistance in Salmonella enterica recovered from cattle minced meat and rabbit meat. Overall, the highest incidence rate of Salmonella enterica was found in cattle-derived products, and it was slightly more prevalent in RTE/D foods than in raw foods. Resistance to critical and clinically important antibiotics, particularly in Salmonella from RTE/D food, suggests that these antibiotics are being abused in the investigated area's veterinary field, and raises the potential of these isolates being transmitted to high-risk humans, which would be a serious problem. Future research using whole-genome sequencing is needed to clarify Salmonella resistance mechanisms to critically important antimicrobial agents or those exhibiting multidrug resistance. This article is protected by copyright. All rights reserved.

The Invasin and Complement-Resistance Protein Rck of Salmonella is More Widely Distributed than Previously Expected

The rck open reading frame (ORF) on the pefI-srgC operon encodes an outer membrane protein responsible for invasion of nonphagocytic cell lines and resistance to complement-mediated killing. Until now, the rck ORF was only detected on the virulence plasmids of three serovars of Salmonella subsp. enterica (i.e., Bovismorbificans, Enteritidis, and Typhimurium). The increasing number of Salmonella genome sequences allowed us to use a combination of reference sequences and whole-genome multilocus sequence typing (wgMLST) data analysis to probe the presence of the operon and of rck in a wide array of isolates belonging to all Salmonella species and subspecies. We established the presence of partial or complete operons in 61 subsp. enterica serovars as well as in 4 other subspecies with various syntenies and frequencies. The rck ORF itself was retrieved in 36 subsp. enterica serovars and in two subspecies with either chromosomal or plasmid-borne localization. It displays high conservation of its sequence within the genus, and we demonstrated that most of the allelic variations identified did not alter the virulence properties of the protein. However, we demonstrated the importance of the residue at position 38 (at the level of the first extracellular loop of the protein) in the invasin function of Rck. Altogether, our results highlight that rck is not restricted to the three formerly identified serovars and could therefore have a more important role in virulence than previously expected. Moreover, this work raises questions about the mechanisms involved in rck acquisition and about virulence plasmid distribution and evolution.

IMPORTANCE The foodborne pathogen Salmonella is responsible for a wide variety of pathologies depending on the infected host, the infecting serovars, and its set of virulence factors. However, the implication of each of these virulence factors and their role in the specific host-pathogen interplay are not fully understood. The significance of our research is in determining the distribution of one of these factors, the virulence plasmid-encoded invasin and resistance to complement killing protein Rck. In addition to providing elements of reflection concerning the mechanisms of acquisition of specific virulence genes in certain serotypes, this work will help to understand the role of Rck in the pathogenesis of Salmonella.

Analysis of the assessment of antimicrobial susceptibility. Non-typhoid Salmonella in meat and meat products as model (systematic review)

BACKGROUND

The scientific publications of antimicrobial susceptibilities and resistance must be precise, with interpretations adjusted to the standard. In this frame, knowledge of antimicrobial resistance is fundamental in pathogenic microorganisms such as Salmonella spp., known for many annual deaths worldwide. The objective of this work was to compare the interpretation of standards, the concentrations, and the breakpoints, to study antimicrobial resistance in Non-Typhoidal Salmonella (NTS) isolated from beef, pork, and chicken meat, meat products, and propose additional considerations that improve the use and usefulness of published results.

RESULTS

After refining the search based on meeting the inclusion and exclusion criteria, 48 papers were selected. In 33 (68.8%) of them, the disc diffusion method was used, in 11 (22.9%) the MIC determination method, and in 4 (8.33%) were used both. In 24 (50%) of the articles, the selection of a different (correct) standard could have had an impact on the interpretation of antimicrobial susceptibility, which observed when considering three scenarios, i) comparison between the year of the isolation versus the implemented standard, ii) comparison between the year of submission versus implemented standard and iii) comparison between the year of publication versus implemented standard.

CONCLUSIONS

The most frequent scenario was the inadequate selection of standards, indicating that some studies had not ensured that applied standards kept in line with the date of isolation, date of publication and interpretation of susceptibilities. We proposed 2 years for standards use for resistance and multi-resistance interpretations. On the other hand, we invite researchers to publish their results in the shortest possible time, and editors and reviewers of scientific journals to prioritise these types of studies and verify the correspondence between the standard cited and the one used and the one to be taken into account.

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.

Characterization of Salmonella spp. isolated from chickens in Central China

Background

Salmonella is an important zoonotic pathogen, and chickens are one of its main hosts. Every year, Salmonella infections pose a serious threat to the poultry industry in developing countries, especially China. In this study, a total of 84 Salmonella isolates recovered from sick and healthy-looking chickens in central China were characterized by serotyping, MLST-based strain typing, presence of potential virulence factors, and antimicrobial resistance profiles.

Result

Data showed that the main serotypes of Salmonella isolates in central China were Salmonella enterica serovar Gallinarum biovar Pullorum, Salmonella enterica serovar Gallinarum biovar Gallinarum, Salmonella enterica serovar Enteritidis and Salmonella enterica serovar Typhimurium, and among them, S. Pullorum was the dominant type in both sick and healthy-looking chickens, accounting for 43.9 and 46.5%, respectively, while S. Enteritidis was only found in healthy-looking chickens. All isolates exhibited higher resistance rates to ampicillin (97.6%), tetracycline (58.3%) and colistin (51.2%), and among these isolates, 49.5% were resistant to more than three drugs in different combinations. S. Enteritidis was the most severe multidrug-resistant serotype, which showed higher resistance rates to colistin, meropenem and ciprofloxacin. Multilocus sequence typing (MLST) revealed that S. Gallinarum and S. Enteritidis isolates were clustered in clade 1, which belonged to two and one STs, respectively. All S. Typhimurium isolates were clustered in clade 3, and belonged to three STs. However, S. Pullorum were distributed in three clades, which belonged to 7 STs. Twenty-seven virulence-associated genes were detected, and expected cdtB, which was absent in all the isolates, the other 26 genes were conserved in the closely related Salmonella serogroup D (S. Enteritidis, S. Pullorum, and S. Gallinarum).

Conclusion

Salmonella serogroup D was the major subgroup, and S. Pullorum was the most common type in sick and healthy-looking chickens in central China. Drug resistance assays showed serious multiple antimicrobial resistances, and S. Enteritidis was the most severe drug-resistant serotype. MLST showed that there was correlation between serotypes and genotypes in most Salmonella isolates, except S. Pullorum, which showed complicated genetic diversity firstly. These results provide important epidemiological information for us to control Salmonella in chickens.

Cell-free supernatants from cultures of lactic acid bacteria isolated from fermented grape as biocontrol against Salmonella Typhi and Salmonella Typhimurium virulence via autoinducer-2 and biofilm interference

Background

Salmonella Typhi and Salmonella Typhimurium are the causative pathogens of salmonellosis, and they are mostly found in animal source foods (ASF). The inappropriate use of antibiotics enhances the possibility for the emergence of antibiotic resistance in pathogens and antibiotic residue in ASF. One promising alternative to antibiotics in animal farming is the use of lactic acid bacteria (LAB).

Methods

The present study was carried out the cells and/or the cell-free culture supernatants (CFCS) from beneficial LAB against S. Typhi and S. Typhimurium. The antibacterial mechanisms of LAB-CFCS as biocontrol agents against both Salmonella serovars were investigated through the analysis of anti-salmonella growth activity, biofilm inhibition and quorum quenching activity.

Results

Among 146 LAB strains isolated from 110 fermented food samples, the 2 strong inhibitory effect strains (WM33 and WM36) from fermented grapes against both Salmonella serovars were selected. Out of the selected strains, WM36 was the most effective inhibitor, which indicated S. Typhi by showing 95.68% biofilm inhibition at 20% biofilm inhibition concentration (BIC) and reduced 99.84% of AI-2 signaling interference. The WM33 was the best to control S. Typhimurium by producing 66.46% biofilm inhibition at only 15% BIC and 99.99% AI-2 signaling a reduction. The 16S rDNA was amplified by a polymerase chain reaction (PCR). The selected isolates were identified as Weissella viridescens WM33 and Weissella confusa WM36 based on nucleotide homology and phylogenetic analysis.

Conclusion

The metabolic extracts from Weissella spp. inhibit Salmonella serovars with the potential to be used as biocontrol agents to improve microbiological safety in the production of ASF.

Prevalence, molecular characterization, and antimicrobial resistance profiles of Listeria monocytogenes, Salmonella enterica, and Escherichia coli O157:H7 on dairy cattle farms in Jordan

This study determined the prevalence, pulsed-field gel electrophoresis profiles, and antimicrobial resistance profile of Listeria monocytogenes, Salmonella enterica, and Escherichia coli O157:H7 isolates from dairy cattle farms in Jordan. Samples from bulk tank milk (n = 305), cattle feces (n = 610), and rectoanal mucosal swabs (n = 610) were collected from 61 dairy cattle farms. We confirmed 32 L. monocytogenes, 28 S. enterica, and 24 E. coli O157:H7 isolates from the samples. The farm-level prevalence (at least 1 positive sample per farm) of L. monocytogenes, S. enterica, and E. coli O157:H7 was 27.9, 19.7, and 23.0%, respectively. The prevalence of L. monocytogenes, S. enterica, and E. coli O157:H7 in bulk tank milk was 7.5, 1.6, and 3.3%, respectively. The prevalence of L. monocytogenes and S. enterica in fecal samples was 1.5 and 3.8%, respectively, and the prevalence of E. coli O157:H7 in rectoanal mucosal swabs was 2.3%. Based on disk diffusion testing, all L. monocytogenes, S. enterica, and E. coli O157:H7 isolates exhibited resistance to at least 1 antimicrobial class. Multidrug resistance (resistance to 3 or more classes of antimicrobials) was exhibited by 96.9% of L. monocytogenes, 91.7% of E. coli O157:H7, and 82.1% of S. enterica isolates. Moreover, 93.8, 79.2, and 57.1% of the L. monocytogenes, E. coli O157:H7, and S. enterica isolates, respectively, were resistant to 5 or more antimicrobial classes. More than 50% of L. monocytogenes isolates were resistant to ampicillin, clindamycin, penicillin, erythromycin, quinupristin-dalfopristin, streptomycin, teicoplanin, linezolid, vancomycin, kanamycin, and tetracycline. More than 50% of S. enterica and E. coli O157:H7 isolates were resistant to ampicillin, cephalothin, nalidixic acid, kanamycin, streptomycin, amoxicillin-clavulanic acid, and tetracycline. The prevalence of the studied pathogens this study was comparable to reports from other countries. The isolated pathogens exhibited a high degree of antimicrobial resistance, suggesting that the bacterial flora of dairy cattle in Jordan are under intense antimicrobial selection pressure. Additional research is required to determine the causes and drivers of resistance, and to develop approaches to mitigating antimicrobial resistance.

Characterization of Antimicrobial Resistant (AMR) Salmonella Enterica Isolates Associated With Cattle at Harvest in Mexico

Despite being the target of control efforts for many decades, Salmonella enterica continues to be linked with a large amount of foodborne illnesses and outbreaks worldwide. Over the years, Salmonella isolated from meat products have exhibited a high level of antibiotic resistance. In this study, a total of 351 Salmonella isolates, recovered from cattle fecal samples (n = 31), hides (n = 105), and beef carcasses (n = 215) from 3 abattoirs in Mexico were analyzed for antimicrobial susceptibility. Resistance to at least one antimicrobial drug was found in 205 (58.4%) isolates and 20 different resistance phenotypes were observed among this Salmonella isolates set. Resistance to tetracycline (40.2%) and nalidixic acid (21.1%) was most commonly observed. Additionally, the most common multidrug-resistant (MDR) phenotypes shared resistance to chloramphenicol, streptomycin, tetracycline, and trimethopin/sulfamethoxazole (11.3%), resistance to ampicillin, tetracycline, and trimethopin/sulfamethoxazole (3.4%), and resistance to ampicillin, streptomycin, and tetracycline (2.5%). When it came to antimicrobial resistance phenotypes in each abattoir, we determined there was no statistical difference in the frequency of resistant vs. susceptible Salmonella isolates among the three abattoirs (P > 0.05). These data indicate that Salmonella isolates recovered from beef cattle in Mexico are commonly resistant to antimicrobials and often multiple antimicrobials. In Mexico, antimicrobial resistance, and in particular, multidrug-resistance, maybe of particular concern due to the much higher prevalence of Salmonella in retail beef. This may lead to the spread of resistance and to the reduction of antibiotic efficacy for the control of animal and human infections. Promoting control measures and inspection standards on imported animals and food products should be applied to avoid the spread of antibiotic resistance in various populations and among countries.

Antimicrobial Resistance in Commensal Escherichia coli Isolated from Pigs and Pork Derived from Farms Either Routinely Using or Not Using In-Feed Antimicrobials

The aims of this study were (i) to evaluate whether routine in-feed antimicrobial use in pigs or not resulted in differences in antimicrobial resistance (AMR) E. coli at different pig producing stages, and (ii) to determine whether resistant strains were presented in pig meat postslaughter. A total of 300 commensal E. coli isolates were obtained and examined for antibiograms, AMR genes, plasmid replicons, and molecular types. The isolates were from two farms either using (A) or not using in-feed antimicrobials (NA), sampled four times during the production cycle and once postslaughter. E. coli resistant to aminoglycosides containing aadA1, aadA2, and aadB and extended-spectrum beta-lactamase-producing (ESBLP) E. coli containing bla_CTX-M-1 were significantly increased in the nursery and growing periods in farm A compared to farm NA. IncI1-Iγ and IncHI2 were common in the nursery period and were shown to transfer bla_CTX-M genes by conjugation. ST10 was the most common type only found in live pigs. ST604, ST877, ST1209, and ST2798 ESBLP were found only in live pigs, whereas ST72, ST302, and ST402 ESBLP were found in pig meat.

Distribution of virulence factors, determinants of antibiotic resistance and molecular fingerprinting of Salmonella species isolated from cattle and beef samples: suggestive evidence of animal-to-meat contamination

In this study, three hundred presumptive Salmonella strains isolated from cattle faeces and raw beef samples were subjected to both preliminary and confirmatory tests specific for Salmonella. PCR assays revealed that 100%, 20% and 26.7% of the isolates were positive for 16S rRNA, fliC and fljB gene fragments, respectively. Large proportions (62.4 to 94.3%) of these isolates were multiple antibiotic resistant (MAR) strains that were resistant to three or more antibiotics belonging to different classes. MAR phenotypes Ab1, Ab2, Ab3, Ab7, Ab8, Ab9, Ab26 and Ab27 were dominant among the isolates. Cluster analysis of antibiotic inhibition zone diameter data revealed two major clusters (clusters 1 and 2), and each cluster contained two sub-clusters (1A, 1B, 2A and 2B). PCR data revealed that 27.1% and 30.7% of the isolates possessed the spvC and invA virulent genes, respectively. There was a significant correlation between the possession of MAR phenotypes and virulent gene determinants. Analysis of restriction fragment length polymorphism (RFLP) of 16S rRNA gene fragments using EcoRI and HaeIII showed that large proportions of isolates from beef and cattle faeces produced similar genetic fingerprints. From these results, it is suggested that Salmonella species in cattle are transmitted to beef and, therefore, the consumption of undercooked beef could pose severe health complications on consumers. These findings provide baseline data that could be of great epidemiological importance and, thus, the need to utilise more sensitive typing tools in determining the genetic relatedness of isolates from different sources.

Phenotypic and genotypic antimicrobial resistance and virulence genes of Salmonella enterica isolated from pet dogs and cats

Salmonella enterica isolates (n = 122), including 32 serotypes from 113 dogs and 9 cats, were obtained from household dogs (n = 250) and cats (n = 50) during 2012-2015. The isolates were characterized by serotyping, antimicrobial resistance phenotyping and genotyping, and virulence gene screening. Serovars Weltevreden (15.6%) and Typhimurium (13.9%) were the most common. The majority (43%) of the isolates were multidrug resistant. The dog isolates (12.3%) harbored class 1 integrons, of which the dfrA12-aadA2 cassette was most frequent (66.7%). The only class integron in serovar Albany was located on a conjugative plasmid. Two ESBL-producing isolates (i.e., a serovar Krefeld and a serovar Enteritridis) carried bla_TEM and bla_CTX-M, and the bla_TEM gene in both was horizontally transferred. Of the plasmid-mediated quinolone resistance genes tested, only qnrS (4.9%) was detected. Most Salmonella isolates harbored invA (100%), prgH (91.8%), and sipB (91%). Positive associations between resistance and virulence genes were observed for bla_PSE-1/orgA, cmlA/span, tolC, and sul1/tolC (p ＜ 0.05). The results suggest that companion dogs and cats are potential sources of S. enterica strains that carry resistance and virulence genes and that antimicrobial use in companion animals may select for the examined Salmonella virulence factors.

Routine Prophylactic Antimicrobial Use Is Associated with Increased Phenotypic and Genotypic Resistance in Commensal Escherichia coli Isolates Recovered from Healthy Fattening Pigs on Farms in Thailand

This study examined antimicrobial resistance (AMR) profiles in commensal Escherichia coli derived from healthy fattening pigs in Thai farms that used prophylactic antimicrobials (in-feed tiamulin fumarate and amoxicillin) [PAs], therapeutic antimicrobials (injectable enrofloxacin or gentamicin) [TAs], or no antimicrobials [NAs]. Commensal E. coli were used as a proxy for overall AMR on the farms. There was a high level of multidrug resistance in all three categories of farm, with isolates showing resistance to β-lactams (amoxicillin, ampicillin, and piperacillin) and tetracyclines (tetracycline), and commonly possessing tetA, bla_TEM, and plasmid replicons FIB and F. On the other hand, isolates with an extended-spectrum beta-lactamase phenotype (ESBLP) and with resistance to aminoglycosides, chloramphenicol, fluoroquinolones, nitrofurantoin, tiamulin, and trimethoprim/sulfamethoxazole were significantly more common among the PA farms (p < 0.05) than in the other two farm categories. In the PA farms, ESBLP E. coli commonly contained the bla_CTX-M-1 group, bla_CTX-M-9 group, or both gene groups, and were shown to transfer bla_CTX-M genes in a conjugation experiment. E. coli containing N, FIC and A/C replicons were found only in PA farms. In summary, although E. coli isolates from all farms contained a core set of resistance to β-lactams and tetracyclines, the routine use of PA increased resistance rates to other important antimicrobials.

Characterization of Virulence-Associated Genes, Antimicrobial Resistance Genes, and Class 1 Integrons in Salmonella enterica serovar Typhimurium Isolates from Chicken Meat and Humans in Egypt

Foodborne pathogens are leading causes of illness especially in developing countries. The current study aimed to characterize virulence-associated genes and antimicrobial resistance in 30 Salmonella Typhimurium isolates of chicken and human origin at Mansoura, Egypt. The results showed that invA, avrA, mgtC, stn, and bcfC genes were identified in all the examined isolates, while 96.7% and 6.7% were positive for sopB and pef genes, respectively. The highest resistance frequencies of the isolates were to chloramphenicol and trimethoprim-sulfamethoxazole (73.3%, each), followed by streptomycin (56.7%), tetracycline and ampicillin (53.3%, each), and gentamicin (30%). However, only 2.7% of the isolates were resistant to cefotaxime and ceftriaxone each. Different resistance-associated genes, including blaTEM, aadB, aadC, aadA1, aadA2, floR, tetA(A), tetA(B), and sul1, were identified in Salmonella Typhimurium isolates with the respective frequencies of 53.3%, 6.7%, 23.3%, 46.7%, 63.3%, 73.3%, 60%, 20%, and 96.7%. None of the isolates was positive for blaSHV, blaOXA, and blaCMY genes. The results showed that the intI1 gene was detected in 24 (80%) of the examined Salmonella Typhimurium isolates. Class 1 integrons were found in 19 (79.2%) isolates that were intI1 positive. Seven integron profiles (namely: P-I to P-VII) were identified with P-V (gene cassette dfrA15, aadA2), the most prevalent profile. To the best of our knowledge, this is the first study to characterize the unusual gene cassette array dfrA12-OrfF-aadA27 from Salmonella Typhimurium isolates in Egypt.

Intensified food production and correlated risks to human health in the Greater Mekong Subregion: a systematic review

BACKGROUND

Intensified food production, i.e. agricultural intensification and industrialized livestock operations may have adverse effects on human health and promote disease emergence via numerous mechanisms resulting in either direct impacts on humans or indirect impacts related to animal and environmental health. For example, while biodiversity is intentionally decreased in intensive food production systems, the consequential decrease in resilience in these systems may in turn bear increased health risks. However, quantifying these risks remains challenging, even if individual intensification measures are examined separately. Yet, this is an urgent task, especially in rapidly developing areas of the world with few regulations on intensification measures, such as in the Greater Mekong Subregion (GMS).

METHODS

We systematically searched the databases PubMed and Scopus for recent studies conducted on the association between agricultural (irrigation, fertilization, pesticide application) and livestock (feed additives, animal crowding) intensification measures and human health risks in the GMS. The search terms used were iteratively modified to maximize the number of retrieved studies with relevant quantitative data.

RESULTS

We found that alarmingly little research has been done in this regard, considering the level of environmental contamination with pesticides, livestock infection with antibiotic resistant pathogens and disease vector proliferation in irrigated agroecosystems reported in the retrieved studies. In addition, each of the studies identified focused on specific aspects of intensified food production and there have been no efforts to consolidate the health risks from the simultaneous exposures to the range of hazardous chemicals utilized.

CONCLUSIONS

While some of the studies identified already reported environmental contamination bearing considerable health risks for local people, at the current state of research the actual consolidated risk from regional intensification measures cannot be estimated. Efforts in this area of research need to be rapidly and considerably scaled up, keeping pace with the current level of regional intensification and the speed of pesticide and drug distribution to facilitate the development of agriculture related policies for regional health promotion.

Prevalence of drug resistance and virulence features in Salmonella spp. isolated from foods associated or not with salmonellosis in Brazil

Salmonella is the most common etiological agent of cases and outbreaks of foodborne diarrheal illnesses. The emergence and spread of Salmonella spp., which has become multi-drug resistant and potentially more pathogenic, have increased the concern with this pathogen. In this study, 237 Salmonella spp., associated or not with foodborne salmonellosis in Brazil, belonging mainly to serotype Enteritidis, were tested for antimicrobial susceptibility and the presence of the virulence genes spvC, invA, sefA and pefA. Of the isolates, 46.8% were sensitive to all antimicrobials and 51.9% were resistant to at least one antimicrobial agent. Resistance to more than one antimicrobial agent was observed in 10.5% of the strains. The highest rates of resistance were observed for streptomycin (35.9%) and nalidixic acid (16.9%). No strain was resistant to cefoxitin, cephalothin, cefotaxime, amikacin, ciprofloxacin and imipenem. The invA gene was detected in all strains. Genes spvC and pefA were found in 48.1% and 44.3% of strains, respectively. The gene sefA was detected in 31.6% of the strains and only among S. Enteritidis. Resistance and virulence determinants were detected in Salmonella strains belonging to several serotypes. The high rates of antibiotic-resistance in strains isolated from poultry products demonstrate the potential risk associated with the consumption of these products and the need to ensure good food hygiene practices from farm to table to reduce the spread of pathogens relevant to public health.

The complete plasmid sequences of Salmonella enterica serovar Typhimurium U288

Salmonella enterica Serovar Typhimurium U288 is an emerging pathogen of pigs. The strain contains three plasmids of diverse origin that encode traits that are of concern for food security and safety, these include antibiotic resistant determinants, an array of functions that can modify cell physiology and permit genetic mobility. At 148,711 bp, pSTU288-1 appears to be a hybrid plasmid containing a conglomerate of genes found in pSLT of S. Typhimurium LT2, coupled with a mosaic of horizontally-acquired elements. Class I integron containing gene cassettes conferring resistance against clinically important antibiotics and compounds are present in pSTU288-1. A curious feature of the plasmid involves the deletion of two genes encoded in the Salmonella plasmid virulence operon (spvR and spvA) following the insertion of a tnpA IS26-like element coupled to a blaTEM gene. The spv operon is considered to be a major plasmid-encoded Salmonella virulence factor that is essential for the intracellular lifecycle. The loss of the positive regulator SpvR may impact on the pathogenesis of S. Typhimurium U288. A second 11,067 bp plasmid designated pSTU288-2 contains further antibiotic resistance determinants, as well as replication and mobilization genes. Finally, a small 4675 bp plasmid pSTU288-3 was identified containing mobilization genes and a pleD-like G-G-D/E-E-F conserved domain protein that modulate intracellular levels of cyclic di-GMP, and are associated with motile to sessile transitions in growth.

Salmonella phages isolated from dairy farms in Thailand show wider host range than a comparable set of phages isolated from U.S. dairy farms

Salmonella is a zoonotic pathogen with globally distributed serovars as well as serovars predominantly found in certain regions; for example, serovar Weltevreden is rarely isolated in the U.S., but is common in Thailand. Relative to our understanding of Salmonella diversity, our understanding of the global diversity of Salmonella phages is limited. We hypothesized that the serovar diversity in a given environment and farming system will affect the Salmonella phage diversity associated with animal hosts. We thus isolated and characterized Salmonella phages from 15 small-scale dairy farms in Thailand and compared the host ranges of the 62 Salmonella phage isolates obtained with host range diversity for 129 phage isolates obtained from dairy farms in the U.S. The 62 phage isolates from Thailand represented genome sizes ranging from 40 to 200 kb and showed lysis of 6-25 of the 26 host strains tested (mean number of strain lysed=19). By comparison, phage isolates previously obtained in a survey of 15 U.S. dairy farms showed a narrow host range (lysis of 1-17; mean number of strains lysed=4); principal coordinate analysis also confirmed U.S. and Thai phages had distinct host lysis profiles. Our data indicate that dairy farms that differ in management practices and are located on different continents can yield phage isolates that differ in their host ranges, providing an avenue for isolation of phages with desirable host range characteristics for commercial applications. Farming systems characterized by coexistence of different animals may facilitate presence of Salmonella phages with wide host ranges.

Subtype analysis of Salmonella isolated from subclinically infected dairy cattle and dairy farm environments reveals the presence of both human- and bovine-associated subtypes

While it is well established that clinically ill livestock represent a reservoir of Salmonella, the importance of subclinical shedders as sources of human salmonellosis is less well defined. The aims of this study were to assess the subtype diversity of Salmonella in healthy dairy cattle and farm environments and to compare the subtypes isolated from these sources with the Salmonella subtypes associated with clinical human cases in the same geographic area. A total of 1349 Salmonella isolates from subclinical dairy cattle and farm environments (46 farms) were initially characterized by traditional or molecular serotyping and tested for antimicrobial susceptibility. A set of 381 representative isolates was selected for further characterization by pulsed-field gel electrophoresis (PFGE); these isolates represented unique combinations of sampling date, serovar, antimicrobial resistance pattern, farm of origin, and source, to avoid overrepresentation of subtypes that were re-isolated from a given source. These 381 isolates represented 26 Salmonella serovars; the most common serovars were Cerro [(38.8%, 148/381) isolated from 21 farms], Kentucky [16.3%; 10 farms], Typhimurium [9.4%; 7 farms], Newport [7.6%; 8 farms], and Anatum [6.3%; 6 farms]. Among the 381 isolates, 90 (23.6%) were resistant to between 1 and 11 antimicrobial agents, representing 50 different antimicrobial resistance patterns. Overall, 61 XbaI-PFGE types were detected among these 381 isolates, indicating considerable Salmonella diversity on dairy farms. Fourteen PFGE types, representing 12 serovars, exactly matched PFGE types from human isolates, suggesting that subclinically infected dairy cattle could be sources of human disease-associated Salmonella.

Survival of Salmonella enterica in poultry feed is strain dependent

Feed components have low water activity, making bacterial survival difficult. The mechanisms of Salmonella survival in feed and subsequent colonization of poultry are unknown. The purpose of this research was to compare the ability of Salmonella serovars and strains to survive in broiler feed and to evaluate molecular mechanisms associated with survival and colonization by measuring the expression of genes associated with colonization (hilA, invA) and survival via fatty acid synthesis (cfa, fabA, fabB, fabD). Feed was inoculated with 1 of 15 strains of Salmonella enterica consisting of 11 serovars (Typhimurium, Enteriditis, Kentucky, Seftenburg, Heidelberg, Mbandanka, Newport, Bairely, Javiana, Montevideo, and Infantis). To inoculate feed, cultures were suspended in PBS and survival was evaluated by plating samples onto XLT4 agar plates at specific time points (0 h, 4 h, 8 h, 24 h, 4 d, and 7 d). To evaluate gene expression, RNA was extracted from the samples at the specific time points (0, 4, 8, and 24 h) and gene expression measured with real-time PCR. The largest reduction in Salmonella occurred at the first and third sampling time points (4 h and 4 d) with the average reductions being 1.9 and 1.6 log cfu per g, respectively. For the remaining time points (8 h, 24 h, and 7 d), the average reduction was less than 1 log cfu per g (0.6, 0.4, and 0.6, respectively). Most strains upregulated cfa (cyclopropane fatty acid synthesis) within 8 h, which would modify the fluidity of the cell wall to aid in survival. There was a weak negative correlation between survival and virulence gene expression indicating downregulation to focus energy on other gene expression efforts such as survival-related genes. These data indicate the ability of strains to survive over time in poultry feed was strain dependent and that upregulation of cyclopropane fatty acid synthesis and downregulation of virulence genes were associated with a response to desiccation stress.

The antibiotic resistance characteristics of non-typhoidal Salmonella enterica isolated from food-producing animals, retail meat and humans in South East Asia

Antimicrobial resistance is a global problem. It is most prevalent in developing countries where infectious diseases remain common, the use of antibiotics in humans and animals is widespread, and the replacement of older antibiotics with new generation antibiotics is not easy due to the high cost. Information on antibiotic resistance phenotypes and genotypes of Salmonella spp. in food animals and humans in different countries and geographic regions is necessary to combat the spread of resistance. This will improve the understanding of antibiotic resistance epidemiology, tracing of new emerging pathogens, assisting in disease treatment, and enhancing prudent use of antibiotics. However, the extent of antibiotic resistance in food-borne pathogens and humans in many developing countries remains unknown. The goal of this review is to discuss the current state of antibiotic resistance of non-typhoid Salmonella spp. in food-producing animals, retail meat and humans from South East Asia. It is focused on resistance characteristics of traditional and "critically important" antibiotics in this region, and the emergence of multidrug resistant strains and genetic elements that contribute to the development of multidrug resistance, including integrons and the Salmonella Genomic Island (SGI).

Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens

Antibiotics were one of the great discoveries of the 20th century. However, resistance appeared even in the earliest years of the antibiotic era. Antibiotic resistance continues to become worse, despite the ever-increasing resources devoted to combat the problem. One of the most important factors in the development of resistance to antibiotics is the remarkable ability of bacteria to share genetic resources via Lateral Gene Transfer (LGT). LGT occurs on a global scale, such that in theory, any gene in any organism anywhere in the microbial biosphere might be mobilized and spread. With sufficiently strong selection, any gene may spread to a point where it establishes a global presence. From an antibiotic resistance perspective, this means that a resistance phenotype can appear in a diverse range of infections around the globe nearly simultaneously. We discuss the forces and agents that make this LGT possible and argue that the problem of resistance can ultimately only be managed by understanding the problem from a broad ecological and evolutionary perspective. We also argue that human activities are exacerbating the problem by increasing the tempo of LGT and bacterial evolution for many traits that are important to humans.