Diversity of multidrug-resistant salmonella enterica strains associated with cattle at harvest in the United States

Antimicrobial resistance of Escherichia coli from dairy farms participating in an antimicrobial stewardship educational program for farm employees

Antimicrobial use in food-producing animals is under increasing scrutiny due to the potential effect on the selection of antimicrobial-resistant bacteria that may be transmitted to humans by direct contact, with the food chain, or the environment. Novel data monitoring commensal Escherichia coli from dairy farms is essential for understanding antimicrobial resistance (AMR) patterns and their association with herd health management practices. The objectives of this study were to: (1) compare the prevalence of antimicrobial resistance in the E. coli isolates from the hospital, fresh, and mid-lactation pens from 18 conventional dairy farms participating in an educational training program in antimicrobial stewardship practices in California and Ohio, and (2) to characterize the prevalence of antimicrobial resistance of commensal E. coli isolated from pooled fecal pat samples before and 3 mo after participating in the educational training program. Pooled fecal pat samples were collected from the hospital pen, the fresh pen (1 to 5 DIM), and the mid-lactation pens (90 to 150 DIM) on conventional dairies in CA (n = 9) and OH (n = 9). Fecal samples were collected as part of a larger study using a quasi-experimental design that assigned farms to the training intervention group (TG; 6 per state) or the control group (CG; 3 per state). For the TG, farm worker(s) identified as having the task of diagnosis and treatment of adult cows on the farm participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 mo after completing the intervention on each of the participating farms (n = 18), followed by culture for E. coli isolation and antimicrobial sensitivity testing using the broth microdilution methodology. Logistic regression models were used to evaluate the association between E. coli antimicrobial resistance patterns with the training intervention and farm-level factors. No effect was observed in the prevalence of resistant isolates between the control and intervention farms after the training was delivered. Isolates from the hospital pens were 2.48 (95% CI: 1.06-6.22, P = 0.03) and 5.61 (95% CI: 1.94-16.91, P < 0.001) times, more likely to be resistant to streptomycin and chloramphenicol, respectively, than isolates from the mid-lactation pens. Our findings indicate there was a higher prevalence of AMR in E. coli associated with the hospital pen within the farm, while the training program for 3 mo did not affect the prevalence of AMR in E. coli on the farms participating in the program. Further research efforts should be conducted to identify factors driving AMR at the pen level, as well as approaches that could be used to reduce the risk of disseminating AMR from sick pens to animals being housed and to other pens on the farm.

Review: Salmonella Dublin in dairy cattle

Salmonella enterica serovar Dublin (S. Dublin) is a bacterium host-adapted to cattle with increasing prevalence in dairy facilities. It can severely affect cattle health, producing high morbidity and mortality in young calves and reducing the performance of mature animals. Salmonella Dublin is difficult to control and eradicate from herds, as it can be shed from clinically normal animals. In addition, S. Dublin is a zoonotic bacterium that can be lethal for humans and pose a risk for human and animal health due to its multi-drug resistant characteristics. This review provides an overview of S. Dublin as a pathogen in dairy facilities, the risk factors associated with infection, and current strategies for preventing and controlling this disease. Furthermore, current gaps in knowledge are also discussed.

Metaphylactic antimicrobial effects on occurrences of antimicrobial resistance in Salmonella, Escherichia coli, and Enterococcus spp. measured longitudinally from feedlot arrival to harvest in high-risk beef cattle

Aims

Our objective was to determine how injectable antimicrobials affected populations of Salmonella enterica, Escherichia coli and Enterococcus spp. in feedlot cattle.

Methods and Results

Two arrival date blocks of high‐risk crossbred beef cattle (n = 249; mean BW = 244 kg) were randomly assigned one of four antimicrobial treatments administered on day 0: sterile saline control (CON), tulathromycin (TUL), ceftiofur (CEF) or florfenicol (FLR). Faecal samples were collected on days 0, 28, 56, 112, 182 and study end (day 252 for block 1 and day 242 for block 2). Hide swabs and subiliac lymph nodes were collected the day before and the day of harvest. Samples were cultured for antimicrobial‐resistant Salmonella, Escherichia coli and Enterococcus spp. The effect of treatment varied by day across all targeted bacterial populations (p ≤ 0.01) except total E. coli. Total E. coli counts were greatest on days 112, 182 and study end (p ≤ 0.01). Tulathromycin resulted in greater counts and prevalence of Salmonella from faeces than CON at study end (p ≤ 0.01). Tulathromycin and CEF yielded greater Salmonella hide prevalence and greater counts of 128ERY^RE. coli at study end than CON (p ≤ 0.01). No faecal Salmonella resistant to tetracyclines or third‐generation cephalosporins were detected. Ceftiofur was associated with greater counts of 8ERY^REnterococcus spp. at study end (p ≤ 0.03). By the day before harvest, antimicrobial use did not increase prevalence or counts for all other bacterial populations compared with CON (p ≥ 0.13).

Conclusions

Antimicrobial resistance (AMR) in feedlot cattle is not caused solely by using a metaphylactic antimicrobial on arrival, but more likely a multitude of environmental and management factors.

Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum β-Lactamase in Escherichia coli from Different Animal Sources

Antimicrobial resistance associated with the spread of plasmid-encoded extended-spectrum β-lactamase (ESBL) genes conferring resistance to third generation cephalosporins is increasing worldwide. However, data on the population of ESBL producing E. coli in different animal sources and their antimicrobial characteristics are limited. The purpose of this study was to investigate potential reservoirs of ESBL-encoded genes in E. coli isolated from swine, beef, dairy, and poultry collected from different regions of the United States using whole-genome sequencing (WGS). Three hundred isolates were typed into different phylogroups, characterized by BOX AIR-1 PCR and tested for resistance to antimicrobials. Of the 300 isolates, 59.7% were resistant to sulfisoxazole, 49.3% to tetracycline, 32.3% to cephalothin, 22.3% to ampicillin, 20% to streptomycin, 16% to ticarcillin; resistance to the remaining 12 antimicrobials was less than 10%. Phylogroups A and B1 were most prevalent with A (n = 92, 30%) and B1 (87 = 29%). A total of nine E. coli isolates were confirmed as ESBL producers by double-disk synergy testing and multidrug resistant (MDR) to at least three antimicrobial drug classes. Using WGS, significantly higher numbers of ESBL-E. coli were detected in swine and dairy manure than from any other animal sources, suggesting that these may be the primary animal sources for ESBL producing E. coli. These isolates carry plasmids, such as IncFIA(B), IncFII, IncX1, IncX4, IncQ1, CollRNAI, Col440I, and acquired ARGs aph(6)-Id, aph(3″)-Ib, aadA5, aph(3')-Ia, bla_CTX-M-15, bla_TEM-1B, mphA, ermB, catA1, sul1, sul2, tetB, dfrA17. One of the E. coli isolates from swine with ST 410 was resistant to nine antibiotics and carried more than 28 virulence factors, and this ST has been shown to belong to an international high-risk clone. Our data suggests that ESBL producing E. coli are widely distributed in different animal sources, but swine and dairy cattle may be their main reservoir.

Antibiotics and Antibiotic Resistance Genes in Animal Manure - Consequences of Its Application in Agriculture

Antibiotic resistance genes (ARGs) are a relatively new type of pollutant. The rise in antibiotic resistance observed recently is closely correlated with the uncontrolled and widespread use of antibiotics in agriculture and the treatment of humans and animals. Resistant bacteria have been identified in soil, animal feces, animal housing (e.g., pens, barns, or pastures), the areas around farms, manure storage facilities, and the guts of farm animals. The selection pressure caused by the irrational use of antibiotics in animal production sectors not only promotes the survival of existing antibiotic-resistant bacteria but also the development of new resistant forms. One of the most critical hot-spots related to the development and dissemination of ARGs is livestock and poultry production. Manure is widely used as a fertilizer thanks to its rich nutrient and organic matter content. However, research indicates that its application may pose a severe threat to human and animal health by facilitating the dissemination of ARGs to arable soil and edible crops. This review examines the pathogens, potentially pathogenic microorganisms and ARGs which may be found in animal manure, and evaluates their effect on human health through their exposure to soil and plant resistomes. It takes a broader view than previous studies of this topic, discussing recent data on antibiotic use in farm animals and the effect of these practices on the composition of animal manure; it also examines how fertilization with animal manure may alter soil and crop microbiomes, and proposes the drivers of such changes and their consequences for human health.

Consecutive Treatments with a Multicomponent Sanitizer Inactivate Biofilms Formed by Escherichia coli O157:H7 and Salmonella enterica and Remove Biofilm Matrix

ABSTRACT

Many foodborne pathogens, including Escherichia coli O157:H7 and Salmonella enterica, can develop biofilms on contact surfaces at meat processing plants. Owing to the high tolerance of the biofilm cells associated with the three-dimensional biofilm structure and the well-expressed bacterial extracellular polymeric substances, it is a real challenge to completely inactivate and remove mature biofilms, as well as further prevent biofilm reoccurrence and pathogen survival. In the present study, we evaluated the effectiveness of consecutive treatments (10 to 120 min per treatment) by repeatedly applying a multicomponent sanitizer, based on a functional mechanism by synergistic combination of hydrogen peroxide and quaternary ammonia compounds, against biofilms formed by E. coli O157:H7 and S. enterica strains. Biofilms on stainless steel surfaces were treated with 2.5, 5, or 10% (recommended working concentration) of the sanitizer applied as a foam or liquid solution. Our results showed that the multicomponent sanitizer significantly (P < 0.05) reduced the amount of viable biofilm cells at all concentrations, as enumerable bacteria were only detected after low-concentration treatments (2.5 or 5%) with short exposure periods (10 or 20 min per treatment). Treatments with high concentrations (5 or 10%) of the sanitizer, multiple consecutive treatments (2 or 3 treatments), and sufficient exposure time (>60 min per treatment) effectively controlled pathogen survival postsanitization. Examination with a scanning electron microscope showed that treatment with the sanitizer at 5% strength significantly dissolved the connecting extracellular polysaccharide matrix and removed the majority of the biofilm matrix. No intact biofilm structure was detected after the 10% sanitizer treatment; instead, scattered individual bacteria with visibly altered cell morphology were observed. The treated bacteria exhibited indented and distorted shapes with shortened cell length and increased surface roughness, indicating severe cell injury and death. Our observations indicated that consecutive treatments with the multicomponent sanitizer was effective in inactivating E. coli O157:H7 and S. enterica biofilms and preventing pathogen reoccurrence.

HIGHLIGHTS

Analysis of Salmonella enterica serovar Enteritidis isolates from chickens and chicken meat products in Malaysia using PFGE, and MLST

BACKGROUND

Salmonella is a very important foodborne pathogen causing illness in humans. The emergence of drug-resistant strains also constitutes a serious worry to global health and livestock productivity. This study investigated Salmonella isolates from chicken and chicken meat products using the phenotypic antimicrobial screening as well as the molecular characteristics of Salmonella isolates. Upon serotyping of the isolates, the antimicrobial susceptibility profiling using a panel of 9 commonly used antimicrobials was done. Subsequently, the molecular profiles of all the isolates were further determined using Pulsed Field Gel Electrophoresis (PFGE) and the Whole Genome Multi-Locus Sequence Type (wgMLST) analysis in order to obtain the sequence types.

RESULTS

The PFGE data was input into FPQuest software, and the dendrogram generated was studied for possible genetic relatedness among the isolates. All the isolates were found to belong to the Salmonella Enteritidis serotype with notable resistance to tetracycline, gentamycin, streptomycin, and sulfadimidine. The S. Enteritidis isolates tested predominantly subtyped into the ST11 and ST1925, which was found to be a single cell variant of ST11. The STs were found to occur in chicken meats, foods, and live chicken cloacal swabs, which may indicate the persistence of the bacteria in multiple foci.

CONCLUSION

The data demonstrate the presence of S. Enteritidis among chickens, indicating its preference and reservoir status for enteric Salmonella pathogens.

Effectiveness and Functional Mechanism of a Multicomponent Sanitizer against Biofilms Formed by Escherichia coli O157:H7 and Five Salmonella Serotypes Prevalent in the Meat Industry

ABSTRACT

Biofilm formation by Escherichia coli O157:H7 and Salmonella enterica at meat processing plants poses a potential risk of meat product contamination. Many common sanitizers are unable to completely eradicate biofilms formed by these foodborne pathogens because of the three-dimensional biofilm structure and the presence of bacterial extracellular polymeric substances (EPSs). A novel multifaceted approach combining multiple chemical reagents with various functional mechanisms was used to enhance the effectiveness of biofilm control. We tested a multicomponent sanitizer consisting of a quaternary ammonium compound (QAC), hydrogen peroxide, and the accelerator diacetin for its effectiveness in inactivating and removing Escherichia coli O157:H7 and Salmonella enterica biofilms under meat processing conditions. E. coli O157:H7 and Salmonella biofilms on common contact surfaces were treated with 10, 20, or 100% concentrations of the multicomponent sanitizer solution for 10 min, 1 h, or 6 h, and log reductions in biofilm mass were measured. Scanning electron microscopy (SEM) was used to directly observe the effect of sanitizer treatment on biofilm removal and bacterial morphology. After treatment with the multicomponent sanitizer, viable E. coli O157:H7 and Salmonella biofilm cells were below the limit of detection, and the prevalence of both pathogens was low. After treatment with a QAC-based control sanitizer, surviving bacterial cells were countable, and pathogen prevalence was higher. SEM analysis of water-treated control samples revealed the three-dimensional biofilm structure with a strong EPS matrix connecting bacteria and the contact surface. Treatment with 20% multicomponent sanitizer for 10 min significantly reduced biofilm mass and weakened the EPS connection. The majority of the bacterial cells had altered morphology and compromised membrane integrity. Treatment with 100% multicomponent sanitizer for 10 min dissolved the EPS matrix, and no intact biofilm structure was observed; instead, scattered clusters of bacterial aggregates were detected, indicating the loss of cell viability and biofilm removal. These results indicate that the multicomponent sanitizer is effective, even after short exposure with dilute concentrations, against E. coli O157:H7 and S. enterica biofilms.

HIGHLIGHTS

Evaluation of Bactericidal Effects of Phenyllactic Acid on Escherichia coli O157:H7 and Salmonella Typhimurium on Beef Meat

Bactericidal effects of various concentrations of phenyllactic acid on Shiga toxin-producing Escherichia coli (STEC), including E. coli O157:H7, O26:H11, O103:H2, and O121:H19, and on Salmonella Typhimurium DT104 in pure culture and microplates assays were studied. Beef cuts were surface sprayed with phenyllactic acid or lactic acid for inactivation of E. coli O157:H7 and Salmonella Typhimurium. The 1.5% phenyllactic acid inactivated all inoculated E. coli O157:H7, O26:H11, O103:H2, and O121:H19 and Salmonella Typhimurium DT104 (>6-log reduction) within 1 min of contact at 21°C, whereas 1.5% lactic acid did not result in microbial reduction. Microplate assays (for STEC and Salmonella Typhimurium DT104 at 10 to 100 CFU per well) indicated that concentrations of 0.25% phenyllactic acid or 0.25% lactic acid inhibited the growth of STEC and Salmonella Typhimurium DT104 incubated at 37°C for 24 h. Treatment of beef with 1.5% lactic acid or 1.5% phenyllactic acid reduced E. coli O157:H7 by 0.22 and 0.38 log CFU/cm², respectively, within 5 min and reduced Salmonella Typhimurium DT104 by 0.12 and 0.86 log CFU/cm², respectively. When meat treated with 1.5% phenyllactic acid was frozen at -20°C, inactivation of E. coli O157 and Salmonella Typhimurium DT104 was enhanced by 1.06 and 1.46 log CFU/cm², respectively. Thus, treatment of beef with 1.5% phenyllactic acid significantly reduced the population of E. coli O157:H7 and Salmonella.

Population Dynamics of Salmonella enterica within Beef Cattle Cohorts Followed from Single-Dose Metaphylactic Antibiotic Treatment until Slaughter

Antibiotic use in cattle can select for multidrug-resistant Salmonella enterica, which is considered a serious threat by the U.S. Centers for Disease Control and Prevention. A randomized controlled longitudinal field trial was designed to determine the long-term effects of a single dose of ceftiofur or tulathromycin on Salmonella population characteristics in cattle feces and peripheral lymph nodes and on hides. A total of 134 beef cattle from two sources were divided among 12 pens, with cattle in each of the 3-pen blocks receiving a single dose of either ceftiofur or tulathromycin or neither (control) on day 0. Fecal samples were collected before treatment (day 0) and repeatedly following treatment until slaughter (day 99+). Hide and lymph node samples were collected at slaughter age. Salmonella prevalence, phenotypic antimicrobial resistance, serotype, and phylogenetic relationships were examined. Multilevel mixed logistic regression models indicated no significant effects (P ≥ 0.218) of metaphylactic antibiotics on the prevalence of Salmonella across sample types. However, there was a significant time effect observed, with prevalence increasing from spring through the midsummer months (P < 0.0001) in feces. The majority of Salmonella isolates were pansusceptible to a panel of 14 antibiotics both before and after treatment. Highly prevalent Salmonella serotypes were Salmonella enterica serovar Montevideo, Salmonella enterica serovar Anatum, Salmonella enterica serovar Cerro, and Salmonella enterica serovar Lubbock across all sample types. Strong pen and cattle source serotype clustering effects were observed among Salmonella isolates originating from fecal, lymph node, and hide samples; however, the potential role of Salmonella isolates from the pen environment prior to animal placement was not assessed in this study.IMPORTANCE Salmonella is a leading bacterial foodborne pathogen, causing a significant number of human infections and deaths every year in the United States. Macrolides and 3rd-generation cephalosporins play critical roles in the treatment of human salmonellosis. Use of these antibiotics in beef cattle can select for resistant bacteria that may enter the food chain or spread from the farm via manure. There is a lack of longitudinal research concerning the long-term effects of metaphylactic antibiotic administration. Here, we assessed Salmonella population dynamics during the feeding period until slaughter following single-dose antibiotic treatment. We found no long-term effects of antibiotic use early in the cattle-feeding period on Salmonella prevalence and antimicrobial resistance at slaughter. We identified the pens in which cattle were housed as the factor that contributed most to Salmonella serotypes being shared; importantly, the dominant strain in each pen changed repeatedly over the entire feeding period.

Infection, colonization and shedding of Campylobacter and Salmonella in animals and their contribution to human disease: A review

Livestock meat and offal contribute significantly to human nutrition as sources of high-quality protein and micronutrients. Livestock products are increasingly in demand, particularly in low- and middle-income settings where economies are growing and meat is increasingly seen as an affordable and desirable food item. Demand is also driving intensification of livestock keeping and processing. An unintended consequence of intensification is increased exposure to zoonotic agents, and a contemporary emerging problem is infection with Campylobacter and Salmonella spp. from livestock (avian and mammalian), which can lead to disease, malabsorption and undernutrition through acute and chronic diarrhoea. This can occur at the farm, in households or through the food chain. Direct infection occurs when handling livestock and through bacteria shed into the environment, on food preparation surfaces or around the house and surroundings. This manuscript critically reviews Campylobacter and Salmonella infections in animals, examines the factors affecting colonization and faecal shedding of bacteria of these two genera as well as risk factors for human acquisition of the infection from infected animals or environment and analyses priority areas for preventive actions with a focus on resource-poor settings.

Quantitative Risk Assessment Model of Human Salmonellosis Resulting from Consumption of Broiler Chicken

(1) Background: Salmonella infections are a major cause of illnesses in the United States. Each year around 450 people die from the disease and more than 23,000 people are hospitalized. Salmonella outbreaks are commonly associated with eggs, meat and poultry. In this study, a quantitative risk assessment model (QRAM) was developed to determine Salmonella infections in broiler chicken. (2) Methods: Data of positive Salmonella infections were obtained from the United States Department of Agriculture (USDA) and the Centers for Disease Control and Prevention (CDC) Foodborne Disease Outbreak Surveillance System, in addition to published literature. The Decision Tools @RISK add-in software was used for various analyses and to develop the QRAM. The farm-to-fork pathway was modeled as a series of unit operations and associated pathogen events that included initial contamination at the broiler house (node 1), contamination at the slaughter house (node 2), contamination at retail (node 3), cross-contamination during serving and cooking (node 4), and finally the dose–response model after consumption. (3) Results: QRAM of Salmonella infections from broiler meat showed highest contribution of infection from the retail node (33.5%). (4) Conclusions: This QRAM that predicts the risk of Salmonella infections could be used as a guiding tool to manage the Salmonella control programs

Genomic surveillance links livestock production with the emergence and spread of multi-drug resistant non-typhoidal Salmonella in Mexico

Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is increasingly common worldwide. While food animals are thought to contribute to the growing antimicrobial resistance (AMR) problem, limited data is documenting this relationship, especially in low and middle-income countries (LMIC). Herein, we aimed to assess the role of non-clinical NTS of bovine origin as reservoirs of AMR genes of human clinical significance. We evaluated the phenotypic and genotypic AMR profiles in a set of 44 bovine-associated NTS. For comparative purposes, we also included genotypic AMR data of additional isolates from Mexico (n = 1,067) that are publicly available. The most frequent AMR phenotypes in our isolates involved tetracycline (40/44), trimethoprim-sulfamethoxazole (26/44), chloramphenicol (19/44), ampicillin (18/44), streptomycin (16/44), and carbenicillin (13/44), while nearly 70% of the strains were MDR. These phenotypes were correlated with a widespread distribution of AMR genes (i.e. tetA, aadA, dfrA12, dfrA17, sul1, sul2, bla-TEM-1, blaCARB-2) against multiple antibiotic classes, with some of them contributed by plasmids and/or class-1 integrons. We observed different AMR genotypes for betalactams and tetracycline resistance, providing evidence of convergent evolution and adaptive AMR. The probability of MDR genotype occurrence was higher in meat-associated isolates than in those from other sources (odds ratio 11.2, 95% confidence interval 4.5-27.9, P < 0.0001). The study shows that beef cattle are a significant source of MDR NTS in Mexico, highlighting the role of animal production on the emergence and spread of MDR Salmonella in LMIC.

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.

Complete Closed Genome Sequences of Three Salmonella enterica subsp. enterica Serovar Dublin Strains Isolated from Cattle at Harvest

Salmonella enterica subsp. enterica serovar Dublin is a host-adapted pathogen for cattle that can cause invasive disease in humans. To facilitate genomic comparisons characterizing virulence determinants of this pathogen, we present the complete genome sequences of three S. Dublin strains isolated from bovine sources at harvest.

Influence of zeolite and superphosphate as additives on antibiotic resistance genes and bacterial communities during factory-scale chicken manure composting

Factory-scale chicken manure composting added with zeolite (F), superphosphate (G), or zeolite and ferrous sulfate (FL) simultaneously, were evaluate for their effects on the behaviors of antibiotic resistance genes (ARGs) and bacterial communities. After composting, ARGs in manure decreased by 67.3% in the control, whereas the reductions were 86.5%, 68.6% and 72.2% in F, G and FL, respectively. ARGs encoding ribosomal protection proteins (tetO, tetB(P), and tetM) were reduced to a greater extent than tetG, tetL, sul1 and sul2. Bacteria pathogens were also effectively removed by composting. Network analysis showed that Firmicutes were the important potential host bacteria for ARGs. The bacterial communities and environmental factors, as well as the intI gene, contributed significantly to the variation of ARGs. The ARGs and integrons were reduced more when zeolite was added than when superphosphate was added; thus, it may be useful for reducing the risks of ARGs in chicken manure.

Phenotypic and genotypic characterization of temporally related nontyphoidal Salmonella strains isolated from humans and food animals in central Ethiopia

Salmonella is one of the common causes of food-borne bacterial illnesses. The primary sources of human nontyphoidal Salmonella (NTS) infection are food animals. This study characterized temporally and spatially related Salmonella isolated during April 2013 to March 2014 from faeces of diarrhoeic human patients in Addis Ababa (n = 68) and food animals (n = 84) in Addis Ababa and surrounding districts (dairy cattle, n = 30; slaughtered cattle, n = 20; poultry, n = 26; swine n = 8). Isolates were serotyped, page typed and tested for antimicrobial susceptibility using Kirby-Bauer disc diffusion method, and genotyped by pulsed-field gel electrophoresis (PFGE). The dominant Salmonella serovars isolated from food animals were S. Saintpaul (38.1%), S. Typhimurium (17.9%) and S. Kentucky (9.5%), whereas in humans, S. Typhimurium (39.7%), S. Virchow (30.9%) and S. Kottbus (10.3%) were frequently isolated. Resistance to streptomycin, sulfisoxazole, tetracycline, ampicillin and cephalothin was higher in animal isolates than human isolates, and mean number of antimicrobials to which isolates were resistant was significantly higher in isolates from cattle and poultry compared to those from humans (p < 0.05). All S. Kentucky isolated from animals and humans were multidrug resistant (MDR) with shared resistance phenotype (AmpCfCipTeSuSNa). Although this study involved small sample size and was not able to show clear epidemiological linkage among isolates from various sources, genotyping by PFGE analysis demonstrated circulation of closely related genotypes of S. Virchow, S. Typhimurium and S. Kentucky among humans and food animals. Detection of related Salmonella isolates from humans and animals, the high MDR status of isolates from animals and close proximity of farms and human residential areas in the absence of appropriate biosecurity present major public health problem. Integrated surveillance of Salmonella serovars in humans and animals and implementation of appropriate hazard analysis and pathogen control strategies along critical points of the food chain from farm to table is recommended.

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain

Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain. Whole-genome sequencing (WGS) of bacterial pathogens has shown potential for epidemiological surveillance, outbreak detection, and infection control. In addition, whole metagenome sequencing (WMS) allows for the culture-independent analysis of complex microbial communities, providing useful information on AMR genes occurrence. Both technologies can assist the tracking of AMR genes and mobile genetic elements, providing the necessary information for the implementation of quantitative risk assessments and allowing for the identification of hotspots and routes of transmission of AMR across the food chain. This review article summarizes the information currently available on the use of WGS and WMS for surveillance of AMR in foodborne pathogenic bacteria and food-related samples and discusses future needs that will have to be considered for the routine implementation of these next-generation sequencing methodologies with this aim. In particular, methodological constraints that impede the use at a global scale of these high-throughput sequencing (HTS) technologies are identified, and the standardization of methods and protocols is suggested as a measure to upgrade HTS-based AMR surveillance schemes.

Phenotypic and Genotypic Eligible Methods for Salmonella Typhimurium Source Tracking

Salmonellosis is one of the most common causes of foodborne infection and a leading cause of human gastroenteritis. Throughout the last decade, Salmonella enterica serotype Typhimurium (ST) has shown an increase report with the simultaneous emergence of multidrug-resistant isolates, as phage type DT104. Therefore, to successfully control this microorganism, it is important to attribute salmonellosis to the exact source. Studies of Salmonella source attribution have been performed to determine the main food/food-production animals involved, toward which, control efforts should be correctly directed. Hence, the election of a ST subtyping method depends on the particular problem that efforts must be directed, the resources and the data available. Generally, before choosing a molecular subtyping, phenotyping approaches such as serotyping, phage typing, and antimicrobial resistance profiling are implemented as a screening of an investigation, and the results are computed using frequency-matching models (i.e., Dutch, Hald and Asymmetric Island models). Actually, due to the advancement of molecular tools as PFGE, MLVA, MLST, CRISPR, and WGS more precise results have been obtained, but even with these technologies, there are still gaps to be elucidated. To address this issue, an important question needs to be answered: what are the currently suitable subtyping methods to source attribute ST. This review presents the most frequently applied subtyping methods used to characterize ST, analyses the major available microbial subtyping attribution models and ponders the use of conventional phenotyping methods, as well as, the most applied genotypic tools in the context of their potential applicability to investigates ST source tracking.

Salmonella Typhimurium DT193 and DT99 are present in great and blue tits in Flanders, Belgium

Endemic infections with the common avian pathogen Salmonella enterica subspecies enterica serovar Typhimurium (Salmonella Typhimurium) may incur a significant cost on the host population. In this study, we determined the potential of endemic Salmonella infections to reduce the reproductive success of blue (Cyanistes caeruleus) and great (Parus major) tits by correlating eggshell infection with reproductive parameters. The fifth egg of each clutch was collected from nest boxes in 19 deciduous forest fragments. Out of the 101 sampled eggs, 7 Salmonella Typhimurium isolates were recovered. The low bacterial prevalence was reflected by a similarly low serological prevalence in the fledglings. In this study with a relatively small sample size, presence of Salmonella did not affect reproductive parameters (egg volume, clutch size, number of nestlings and number of fledglings), nor the health status of the fledglings. However, in order to clarify the impact on health and reproduction a larger number of samples have to be analyzed. Phage typing showed that the isolates belonged to the definitive phage types (DT) 193 and 99, and multi-locus variable number tandem repeat analysis (MLVA) demonstrated a high similarity among the tit isolates, but distinction to human isolates. These findings suggest the presence of passerine-adapted Salmonella strains in free-ranging tit populations with host pathogen co-existence.

Population dynamics of enteric Salmonella in response to antimicrobial use in beef feedlot cattle

A randomized controlled longitudinal field trial was undertaken to assess the effects of injectable ceftiofur crystalline-free acid (CCFA) versus in-feed chlortetracycline on the temporal dynamics of Salmonella enterica spp. enterica in feedlot cattle. Two replicates of 8 pens (total 176 steers) received one of 4 different regimens. All, or one, out of 11 steers were treated with CCFA on day 0 in 8 pens, with half of the pens later receiving three 5-day regimens of chlortetracycline from day 4 to day 20. Salmonella was isolated from faecal samples and antimicrobial susceptibility was analysed via microbroth dilution. Serotype was determined by whole-genome sequencing. On day 0, mean Salmonella prevalence was 75.0% and the vast majority of isolates were pansusceptible. Both antimicrobials reduced overall prevalence of Salmonella; however, these treatments increased the proportion of multi-drug resistant (MDR) Salmonella from day 4 through day 26, which was the last day of faecal collection. Only six Salmonella serotypes were detected. Salmonella serotype Reading isolates were extensively MDR, suggesting a strong association between serotype and resistance. Our study demonstrates that the selection pressures of a 3^rd generation cephalosporin and chlortetracycline during the feeding period contribute to dynamic population shifts between antimicrobial susceptible and resistant Salmonella.

Occurrence of Salmonella enterica and Escherichia coli in raw chicken and beef meat in northern Egypt and dissemination of their antibiotic resistance markers

BACKGROUND

The global incidence of foodborne infections and antibiotic resistance is recently increased and considered of public health concern. Currently, scarcely information is available on foodborne infections and ESBL associated with poultry and beef meat in Egypt.

METHODS

In total, 180 chicken and beef meat samples as well as internal organs were collected from different districts in northern Egypt. The samples were investigated for the prevalence and antibiotic resistance of Salmonella enterica serovars and Escherichia coli. All isolates were investigated for harbouring class 1 and class 2 integrons.

RESULTS

Out of 180 investigated samples 15 S. enterica (8.3%) and 21 E. coli (11.7%) were isolated and identified. S. enterica isolates were typed as 9 S. Typhimurium (60.0%), 3 S. Paratyphi A (20.0%), 2 S. Enteritidis (13.3%) and 1 S. Kentucky (6.7%). Twenty-one E. coli isolates were serotyped into O1, O18, O20, O78, O103, O119, O126, O145, O146 and O158. The phenotypic antibiotic resistance profiles of S. enterica serovars to ampicillin, cefotaxime, cefpodoxime, trimethoprim/sulphamethoxazole and tetracycline were 86.7, 80.0, 60.0, 53.3 and 40.0%, respectively. Isolated E. coli were resistant to tetracycline (80.9%), ampicillin (71.4%), streptomycin, trimethoprim/sulphamethoxazole (61.9% for each) and cefotaxime (33.3%). The dissemination of genes coding for ESBL and AmpC β-lactamase in S. enterica isolates included bla_CTX-M (73.3%), bla_TEM (73.3%) and bla_CMY (13.3%). In E. coli isolates bla_TEM, bla_CTX-M and bla_OXA were identified in 52.4, 42.9 and 14.3%, respectively. The plasmid-mediated quinolone resistance genes identified in S. enterica were qnrA (33.3%), qnrB (20.0%) and qnrS (6.7%) while qnrA and qnrB were detected in 33.3% of E. coli isolates. Class 1 integron was detected in 13.3% of S. enterica and in 14.3% of E. coli isolates. Class 2 integron as well as the colistin resistance gene mcr-1 was not found in any of E. coli or S. enterica isolates.

CONCLUSIONS

This study showed high prevalence of S. enterica and E. coli as foodborne pathogens in raw chicken and beef meat in Nile Delta, Egypt. The emergence of antimicrobial resistance in S. enterica and E. coli isolates is of public health concern in Egypt. Molecular biological investigation elucidated the presence of genes associated with antibiotic resistance as well as class 1 integron in S. enterica and E. coli.

Biofilm Formation, Antimicrobial Resistance, and Sanitizer Tolerance of Salmonella enterica Strains Isolated from Beef Trim

In the beef industry, product contamination by Salmonella enterica is a serious public health concern, which may result in human infection and cause significant financial loss due to product recalls. Currently, the precise mechanism and pathogen source responsible for Salmonella contamination in commercial establishments are not well understood. We characterized 89 S. enterica strains isolated from beef trim with respect to their biofilm-forming ability, antimicrobial resistance, and biofilm cell survival/recovery growth after sanitizer exposure. A total of 28 Salmonella serovars was identified within these strains. The most common serovars identified were Anatum, Dublin, Montevideo, and Typhimurium, with these accounting for nearly half of the total strains. The vast majority (86%) of the strains was able to develop strong biofilms, and the biofilm-forming ability was highly strain dependent and related to cell surface expression of extracellular polymeric structures. These strains also demonstrated strong tolerance to quaternary ammonium chloride (QAC) and chlorine dioxide (ClO₂), but were more sensitive to chlorine treatment. Sanitizer tolerance and bacterial postsanitization recovery growth were closely associated with strains' biofilm-forming ability. Thirty percent of the examined strains were found resistant to multiple antimicrobial agents and the resistance phenotypes were serovar associated, but not related to strains' biofilm-forming ability. Pulsed-field gel electrophoresis analysis tended to group strains by serovar rather than by biofilm-forming ability. Collectively, these data indicate that the strong biofilm formers of certain S. enterica strains/serovars possess significant potential for causing meat product contamination in meat processing environment.

Prevalence of antibiotic resistance genes in soils after continually applied with different manure for 30 years

A 30year field experiment with a wheat-soybean cropping system were performed to compare the long-term anthropogenic influence on soil ARGs. Compared with chemical fertilization, the occurrence of 38 ARGs and the abundance of seven ARGs (tetL, tetB(P), tetO, tetW, sul1, ermB, and ermF) were significantly increased by long term exposure of pig manure. However, application of wheat straw and cow manure not substantially affected the abundance of ARGs except cow manure increased the abundance of tetM and tetW to a detectable level. Relative abundance of Firmicutes, Gammaproteobacteria and Bacteroidetes and ARGs observed in the soil were significantly correlated. Integrase gene I1 (intI1) is commonly linked to genes conferring resistance to antibiotics, it was significantly increased in pig manure treated soils and showed a high positive correlation with the abundance of ARGs which were significantly affected by pig manure. Concentrations of Cu, Zn and Pb were also increased in manure treated soil and positive correlated with the relative abundance of intI1 and most of the ARGs. These results indicated that long-term animal manure application to soils has polluted the soil, especially for pig manure, and it should be scrutinized as part of future stewardship programs.

Evaluation of Fecal Indicators and Pathogens in a Beef Cattle Feedlot Vegetative Treatment System

Runoff from open-lot animal feeding areas contains microorganisms that may adversely affect human and animal health if not properly managed. One alternative to full manure containment systems is a vegetative treatment system (VTS) that collects runoff in a sediment basin and then applies it to a perennial vegetation (grass) treatment area that is harvested for hay. Little is known regarding the efficacy of large-scale commercial VTSs for the removal of microbial contaminants. In this study, an active, pump-based VTS designed and built for a 1200-head beef cattle feedlot operation was examined to determine the effects of repeated feedlot runoff application on fecal indicator microorganisms and pathogens over short-term (2 wk) and long-term (3 yr) operations and whether fecal bacteria were infiltrating into deeper soils within the treatment area. In a short-term study, fecal bacteria and pathogen numbers declined over time in soil. Measurements of total coliforms and Enterococcus counts taken on control soils were not effective as fecal indicators. The repeated application of manure-impacted runoff as irrigation water did not enrich the pathogens or fecal indicators in the soil, and no evidence was seen to indicate that pathogens were moving into the deeper soil at this site. These results indicate that large-scale, active VTSs reduce the potential for environmental contamination by manure-associated bacteria. Also, this study has implications to full-containment systems that apply runoff water to land application areas (cropland) and the fate of pathogens in the soils of land application sites.

Prevalence and Characterization of Salmonella enterica and Salmonella Bacteriophages Recovered from Beef Cattle Feedlots in South Texas

Asymptomatic Salmonella carriage in beef cattle is a food safety concern, and the beef feedlot environment may function as a reservoir of this pathogen. The goal of this study was to identify and isolate Salmonella and Salmonella bacteriophages from beef cattle feedlot environments in order to better understand the microbial ecology of Salmonella and identify phages that might be useful as anti-Salmonella beef safety interventions. Three feedlots in south Texas were visited, and 27 distinct samples from each source were collected from dropped feces, feed from feed bunks, drinking water from troughs, and soil in cattle pens (n = 108 samples). Preenrichment, selective enrichment, and selective/differential isolation of Salmonella were performed on each sample. A representative subset of presumptive Salmonella isolates was prepared for biochemical identification and serotyping. Samples were pooled by feedlot and sample type to create 36 samples and enriched to recover phages. Recovered phages were tested for host range against two panels of Salmonella hosts. Salmonella bacteria were identified in 20 (18.5%) of 108 samples by biochemical and/or serological testing. The serovars recovered included Salmonella enterica serovars Anatum, Muenchen, Altona, Kralingen, Kentucky, and Montevideo; Salmonella Anatum was the most frequently recovered serotype. Phage-positive samples were distributed evenly over the three feedlots, suggesting that phage prevalence is not strongly correlated with the presence of culturable Salmonella. Phages were found more frequently in soil and feces than in feed and water samples. The recovery of bacteriophages in the Salmonella-free feedlot suggests that phages might play a role in suppressing the Salmonella population in a feedlot environment.

Salmonella contamination, serovars and antimicrobial resistance profiles of cattle slaughtered in South Africa

Antimicrobial resistant Salmonella are among the leading causes of foodborne infections. Our aim was to determine Salmonella contamination during cattle slaughter in South African rural abattoirs (n = 23) and environmental samples. Furthermore, antimicrobial resistance patterns of the Salmonella isolates were determined. Samples of cattle faeces (n = 400), carcass sponges (n = 100), intestinal contents (n = 62), hides (n = 67), and water from the abattoirs (n = 75) were investigated for Salmonella species using microbiological techniques and species-specific polymerase chain reaction targeting the invA gene. In total 92 Salmonella species isolates were recovered. The Salmonella mean frequency of occurrence on hides, carcasses, and intestinal contents was 35.37% (n = 81). Eleven faecal samples (2.75%) tested positive for Salmonella. The predominant serovar was Salmonella Enteritidis. Diverse serovars that were identified on carcasses were not necessarily found on the hides and intestinal contents. The inconsistent occurrence of the diverse Salmonella serovars on hides, carcasses, and intestinal contents implies that in addition to carriage on hides and in intestinal contents, other external factors also play an important role regarding carcass contamination. The 92 Salmonella were serotyped and tested for susceptibility towards the following antimicrobials: ampicillin, cefotaxime, enrofloxacin, kanamycin, and oxytetracycline using the disk diffusion method. Most Salmonella (n = 66; 71.7%) isolates were resistant to at least one antimicrobial with highest resistance observed towards oxytetracycline (51.90%), which highlights the need for strict hygiene during slaughter and prudent antimicrobial use during animal production. In conclusion, cattle slaughtered in South African rural abattoirs harbour diverse Salmonella serovars that are resistant to antimicrobials, which could be a public health risk. The findings should assist policymakers with improving implementation of hygienic slaughter of cattle in rural abattoirs, which is paramount from socioeconomic, public health, and epidemiological standpoints.

Diagnostic Accuracy of Rectoanal Mucosal Swab of Feedlot Cattle for Detection and Enumeration of Salmonella enterica

Cattle are noted carriers of the foodborne pathogen Salmonella enterica. The perceived need to decrease the potential human health risk posed by excretion of this pathogen has resulted in numerous studies examining the factors that influence Salmonella shedding in cattle. Fecal grab (FG) samples have been the predominant method used to identify cattle colonized or infected with Salmonella; however, FG sampling can be impractical in certain situations, and rectoanal mucosal swabs (RAMS) are a more convenient sample type to collect. Despite a lack of studies comparing FG and RAMS for the detection and enumeration of Salmonella fecal shedding, RAMS is perceived as less sensitive because a smaller amount of feces is cultured. In a cross-sectional study to address these concerns, paired RAMS and FG samples were collected from 403 adult feedlot cattle approximately 90 days prior to harvest. Samples were processed for Salmonella enumeration (direct plating) and detection (enrichment and immunomagnetic separation). In all, 89.6% of RAMS and 98.8% of FG samples were positive for Salmonella, and concordant prevalence outcomes were observed for 90.8% of samples. Mean enumeration values were 3.01 and 3.12 log CFU/ml for RAMS and FG, respectively. The sensitivity and specificity of RAMS were 91% (95% confidence interval [CI]: 87.5 to 93%) and 100% (95% CI: 48 to 100%), respectively, for Salmonella detection. Furthermore, RAMS Salmonella enumeration was substantially concordant (ρc = 0.89; 95% CI: 0.86 to 0.91) with FG values. We conclude that RAMS are a reliable alternative to FG for assessing cattle Salmonella fecal shedding status, especially for cattle shedding high levels of Salmonella.

Prevalence of Nontyphoidal Salmonella and Salmonella Strains with Conjugative Antimicrobial-Resistant Serovars Contaminating Animal Feed in Texas

The objective of this study was to characterize 365 nontyphoidal Salmonella enterica isolates from animal feed. Among the 365 isolates, 78 serovars were identified. Twenty-four isolates (7.0%) were recovered from three of six medicated feed types. Three of these isolates derived from the medicated feed, Salmonella Newport, Salmonella Typhimurium var. O 5- (Copenhagen), and Salmonella Lexington var. 15+ (Manila), displayed antimicrobial resistance. Susceptibility testing revealed that only 3.0% (12) of the 365 isolates displayed resistance to any of the antimicrobial agents. These 12 isolates were recovered from unmedicated dry beef feed (n = 3), medicated dry beef feed (n = 3), cabbage culls (n = 2), animal protein products (n = 2), dry dairy cattle feed (n = 1), and fish meal (n = 1). Only Salmonella Newport and Salmonella Typhimurium var. O 5- (Copenhagen) were multidrug resistant. Both isolates possessed the IncA/C replicon and the blaCMY-2 gene associated with cephalosporin resistance. Plasmid replicons were amplified from 4 of 12 resistant isolates. Plasmids (40 kb) were Salmonella Montevideo and Salmonella Kentucky. Conjugation experiments were done using 7 of the 12 resistant isolates as donors. Only Salmonella Montevideo, possessing a plasmid and amplifying IncN, produced transconjugants. Transconjugants displayed the same antimicrobial resistance profile as did the donor isolate. Three isolates that amplified replicons corresponding to IncA/C or IncHI2 did not produce transconjugants at 30 or 37°C. The results of this study suggest that the prevalence of antimicrobial-resistant Salmonella contaminating animal feed is low in Texas. However, Salmonella was more prevalent in feed by-products; fish meal had the highest prevalence (84%) followed by animal protein products (48%). Ten of the 35 feed types had no Salmonella contamination. Further investigation is needed to understand the possible role of specific feed types in the dissemination of antimicrobial resistant bacteria.

Potential pathogens, antimicrobial patterns and genotypic diversity of Escherichia coli isolates in constructed wetlands treating swine wastewater

Escherichia coli populations originating from swine houses through constructed wetlands were analyzed for potential pathogens, antimicrobial susceptibility patterns, and genotypic diversity. Escherichia coli isolates (n = 493) were screened for the presence of the following virulence genes: stx1, stx2 and eae (Shiga toxin-producing E. coli [STEC]), heat-labile enterotoxin (LT) genes and heat stable toxin STa and STb (enterotoxigenic E. coli (ETEC), cytotoxin necrotizing factors 1 and 2 (cnf1 and cnf2 [necrotoxigenic E. coli- NTEC]), as well as O and H antigens, and the presence of the antibiotic resistance genes blaTEM, blaSHV, blaCMY-2, tet A, tet B, tet C, mph(A), aadA, StrA/B, sul1, sul2 and sul3. The commensal strains were further screened for 16 antimicrobials and characterized by BOX AIR-1 PCR for unique genotypes. The highest antibiotic resistance prevalence was for tetracycline, followed by erythromycin, ampicillin, streptomycin, sulfisoxazole and kanamycin. Our data showed that most of the isolates had high distribution of single or multidrug-resistant (MDR) genotypes. Therefore, the occurrence of MDR E. coli in the wetland is a matter of great concern due to possible transfer of resistance genes from nonpathogenic to pathogenic strains or vice versa in the environment.

Mechanisms of antimicrobial resistant Salmonella enterica transmission associated with starling-livestock interactions

Bird-livestock interactions have been implicated as potential sources for bacteria within concentrated animal feeding operations (CAFO). European starlings (Sturnus vulgaris) in particular are known to contaminate cattle feed and water with Salmonella enterica through their fecal waste. We propose that fecal waste is not the only mechanisms through which starlings introduce S. enterica to CAFO. The goal of this study was to assess if starlings can mechanically move S. enterica. We define mechanical movement as the transportation of media containing S. enterica, on the exterior of starlings within CAFO. We collected 100 starlings and obtained external wash and gastrointestinal tract (GI) samples. We also collected 100 samples from animal pens. Within each pen we collected one cattle fecal, feed, and water trough sample. Isolates from all S. enterica positive samples were subjected to antimicrobial susceptibility testing. All sample types, including 17% of external starling wash samples, contained S. enterica. All sample types had at least one antimicrobial resistant (AMR) isolate and starling GI samples harbored multidrug resistant S. enterica. The serotypes isolated from the starling external wash samples were all found in the farm environment and 11.8% (2/17) of isolates from positive starling external wash samples were resistant to at least one class of antibiotics. This study provides evidence of a potential mechanism of wildlife introduced microbial contamination in CAFO. Mechanical movement of microbiological hazards, by starlings, should be considered a potential source of bacteria that is of concern to veterinary, environmental and public health.

Oral salmonella challenge and subsequent uptake by the peripheral lymph nodes in calves

Previous attempts to infect peripheral lymph nodes (PLNs) with Salmonella via oral inoculation have been inconsistent. Therefore, we performed a series of experiments to determine whether multiple exposures to an oral challenge would result in Salmonella-positive PLN in cattle. In each of three experiments, calves were inoculated with Salmonella Montevideo. In the first experiment, calves were challenged with either no Salmonella (control), a single oral dose (∼10(10); PCON), or 10 consecutive doses in water (∼10(3); WAT). The positive control treatment resulted in an increase (P < 0.05) in the percentage of Salmonella-positive PLNs, compared with the WAT-treated and control animals. Experiments 2 and 3 were designed to additionally determine if the stress associated with feed and water deprivation influences the systemic spread of Salmonella from the gastrointestinal tract to PLNs. Following 14 days of oral inoculation (average 7.1 × 10(4) CFU/day) in experiment 1, Salmonella was recovered from one subiliac and one superficial cervical lymph node of calves that were deprived of feed and water (72 h). No treatment differences (P > 0.05) were observed between control and deprived calves. Based on the poor recovery of Salmonella from the PLNs in WAT-challenged calves in experiments 1 and 2, a higher challenge dose (average 1.2 × 10(7) CFU) was used in experiment 3. The increased dose resulted in the recovery of the challenge strain of Salmonella from the PLNs (70.8 and 75.0% of control and deprived calves, respectively). However, no treatment differences (P > 0.05) were observed between control and deprived calves. Results of this research demonstrated that a substantial oral challenge is required to produce Salmonella-positive PLNs. However, as the challenge periods examined herein were considerably shorter compared with the normal time spent by cattle in feedlots, increased exposure time to lower doses may produce the same effect observed in experiment 3.

A meta-analysis of the proportion of animal Salmonella isolates resistant to drugs used against human salmonellosis in Ethiopia

Background

The emergence and spread of drug resistant Salmonellae of both human and animal origins are global concerns and worrisome in countries where the risk of infection is high and treatment options are limited. The objective of this study was to estimate the proportions of animal isolates resistant to antimicrobials used against human salmonellosis in Ethiopia.

Methods

Published studies on the antimicrobial resistance features of Salmonellae isolated from food animals of Ethiopia were searched in Medline, Google Scholar and the lists of references of articles. Eligible studies were selected by using inclusion and exclusion criteria and data were extracted. The extracted data included the host species, the numbers of isolates and the numbers of ampicillin, co-trimoxazole, chloramphenicol, ceftriaxone and ciprofloxacin resistant isolates. The risks of bias were assessed and the percentages of the variations of the estimates attributable to heterogeneities were quantified. Pooled proportions were estimated by the DerSimonian and Laird random effects model.

Results

Five hundred and fifty four Salmonellae isolated from cattle, camels, sheep, goats and pigs were tested with a variety of antimicrobials. The percentages of the variations attributable to heterogeneities were low for chloramphenicol and ceftriaxone (I² = 0) and high for ampicillin, co-trimoxazole and ciprofloxacin resistance estimates (I² > 75%). The pooled estimate of ampicillin resistant isolates was higher in slaughtered ruminants (17.28%) than in pigs (3.95%), (p < 0.001). The pooled estimates of co-trimoxazole resistant isolates in true ruminants (4.35%) and pigs (1.12%) were not significantly different (p > 0.05). The overall pooled estimates of chloramphenicol and ceftriaxone resistant isolates were 2.24% and 1.25%, respectively. Seven serotypes have been reported to be resistant to antimicrobials uncommonly used in veterinary clinical practice in Ethiopia.

Conclusions

Among Salmonellae of farm animals, there exist strains that are resistant to drugs used in the therapeutic management of human salmonellosis in Ethiopia. Intervention measures should be taken to ensure the prudent use of antimicrobials and curb the spread of high risk strains across the country.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-015-0835-x) contains supplementary material, which is available to authorized users.

Reducing assembly complexity of microbial genomes with single-molecule sequencing

BACKGROUND

The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required to manually close gaps in draft assemblies. Third-generation, single-molecule sequencing addresses this problem by greatly increasing sequencing read length, which simplifies the assembly problem.

RESULTS

To measure the benefit of single-molecule sequencing on microbial genome assembly, we sequenced and assembled the genomes of six bacteria and analyzed the repeat complexity of 2,267 complete bacteria and archaea. Our results indicate that the majority of known bacterial and archaeal genomes can be assembled without gaps, at finished-grade quality, using a single PacBio RS sequencing library. These single-library assemblies are also more accurate than typical short-read assemblies and hybrid assemblies of short and long reads.

CONCLUSIONS

Automated assembly of long, single-molecule sequencing data reduces the cost of microbial finishing to $1,000 for most genomes, and future advances in this technology are expected to drive the cost lower. This is expected to increase the number of completed genomes, improve the quality of microbial genome databases, and enable high-fidelity, population-scale studies of pan-genomes and chromosomal organization.

Occurrence of Antimicrobial-Resistant Escherichia coli and Salmonella enterica in the Beef Cattle Production and Processing Continuum

Specific concerns have been raised that third-generation cephalosporin-resistant (3GC(r)) Escherichia coli, trimethoprim-sulfamethoxazole-resistant (COT(r)) E. coli, 3GC(r) Salmonella enterica, and nalidixic acid-resistant (NAL(r)) S. enterica may be present in cattle production environments, persist through beef processing, and contaminate final products. The prevalences and concentrations of these organisms were determined in feces and hides (at feedlot and processing plant), pre-evisceration carcasses, and final carcasses from three lots of fed cattle (n = 184). The prevalences and concentrations were further determined for strip loins from 103 of the carcasses. 3GC(r) Salmonella was detected on 7.6% of hides during processing and was not detected on the final carcasses or strip loins. NAL(r) S. enterica was detected on only one hide. 3GC(r) E. coli and COT(r) E. coli were detected on 100.0% of hides during processing. Concentrations of 3GC(r) E. coli and COT(r) E. coli on hides were correlated with pre-evisceration carcass contamination. 3GC(r) E. coli and COT(r) E. coli were each detected on only 0.5% of final carcasses and were not detected on strip loins. Five hundred and 42 isolates were screened for extraintestinal pathogenic E. coli (ExPEC) virulence-associated markers. Only two COT(r) E. coli isolates from hides were ExPEC, indicating that fed cattle products are not a significant source of ExPEC causing human urinary tract infections. The very low prevalences of these organisms on final carcasses and their absence on strip loins demonstrate that current sanitary dressing procedures and processing interventions are effective against antimicrobial-resistant bacteria.

Diverse antibiotic resistance genes in dairy cow manure

Application of manure from antibiotic-treated animals to crops facilitates the dissemination of antibiotic resistance determinants into the environment. However, our knowledge of the identity, diversity, and patterns of distribution of these antibiotic resistance determinants remains limited. We used a new combination of methods to examine the resistome of dairy cow manure, a common soil amendment. Metagenomic libraries constructed with DNA extracted from manure were screened for resistance to beta-lactams, phenicols, aminoglycosides, and tetracyclines. Functional screening of fosmid and small-insert libraries identified 80 different antibiotic resistance genes whose deduced protein sequences were on average 50 to 60% identical to sequences deposited in GenBank. The resistance genes were frequently found in clusters and originated from a taxonomically diverse set of species, suggesting that some microorganisms in manure harbor multiple resistance genes. Furthermore, amid the great genetic diversity in manure, we discovered a novel clade of chloramphenicol acetyltransferases. Our study combined functional metagenomics with third-generation PacBio sequencing to significantly extend the roster of functional antibiotic resistance genes found in animal gut bacteria, providing a particularly broad resource for understanding the origins and dispersal of antibiotic resistance genes in agriculture and clinical settings.

The increasing prevalence of antibiotic resistance among bacteria is one of the most intractable challenges in 21st-century public health. The origins of resistance are complex, and a better understanding of the impacts of antibiotics used on farms would produce a more robust platform for public policy. Microbiomes of farm animals are reservoirs of antibiotic resistance genes, which may affect distribution of antibiotic resistance genes in human pathogens. Previous studies have focused on antibiotic resistance genes in manures of animals subjected to intensive antibiotic use, such as pigs and chickens. Cow manure has received less attention, although it is commonly used in crop production. Here, we report the discovery of novel and diverse antibiotic resistance genes in the cow microbiome, demonstrating that it is a significant reservoir of antibiotic resistance genes. The genomic resource presented here lays the groundwork for understanding the dispersal of antibiotic resistance from the agroecosystem to other settings.

Salmonella species in piglets and weaners from Uganda: prevalence, antimicrobial resistance and herd-level risk factors

Non-typhoidal salmonellosis is of concern in humans in sub-Saharan Africa, and this is partly due to the high number of immunocompromised persons. Pork and pork products could be among the sources of these non-typhi Salmonella spp. The aim of this study was to identify Salmonella spp. in piglets and weaners in northern and eastern Uganda, characterize their antimicrobial resistance patterns and determine herd-level risk factors. Fecal samples were collected from 465 piglets and weaners from 93 herds (49 and 44 from northern and eastern Uganda, respectively). In addition, information about the herd management and potential risk factors were collected. The fecal samples were cultured for the identification of Salmonella spp. The Salmonella spp. confirmed by serotyping were further characterized by determination of minimum inhibitory concentration (MIC) to 12 antimicrobials by broth microdilution. At individual level, the total prevalence of Salmonella spp. was 12% (12.2% in northern and 11.9% in eastern Uganda). At herd level, the total prevalence was 39% (43% in northern and 34% in eastern Uganda). From 56 samples with Salmonella spp., 20 serovars were identified including two serovars identified only by their antigenic formulae. The predominant serovars were S. Zanzibar, S. Heidelberg, S. Infantis, S. Typhimurium, S. Stanleyville, S. Aberdeen and S. Kampala. In total, 57% of the 53 Salmonella spp. analyzed, originating from 27% of the herds, were resistant to at least one antimicrobial agent. The majority of drug-resistant isolates (60%) were from northern Uganda. Eight multidrug-resistant (MDR) isolates were from northern Uganda and three MDR isolates were from eastern Uganda. Increased prevalence of Salmonella spp. was associated with feeding the young and adults separately as compared to feeding the young and adults together (p=0.043, OR=4.3; 95% CI 1.1, 17.38). Protective factors were "intensive" method of keeping the pigs versus "tethering and roaming" (p=0.016, OR=0.11; 95% CI 0.02, 0.64), "intensive" method versus "semi-intensive" method (p=0.048, OR=0.12; 95% CI 0.01, 0.96) and cleaning feeders after every two days versus daily (p=0.017, OR=0.18; 95% CI 0.05, 0.72). This study has revealed a high prevalence of infection of piglets and weaners with diverse non-typhi Salmonella serovars and highlights the potential role of pork and pork products as sources of these organisms for humans. In addition, this study has identified protective factors that could be promoted to control Salmonella spp. and in antimicrobial resistance reduction programs in rural pigs from Uganda.

Prevalence and characteristics of Salmonella in the beef chain in the Republic of Ireland

The study investigated the prevalence, concentration and characteristics of Salmonella spp. in the Irish beef chain. A total of 900 samples including bovine hides, carcasses and ground beef were examined for the pathogen over a 2-year study (July 2007-June 2009). Salmonella prevalence was low in all sample types; bovine hide (0.75%, 3 of 400); carcasses (0.25%, 1 of 400); and ground beef (3%, 3 of 100). All positive samples contained the pathogen in low concentrations (<10 CFU per cm(2) or per g). Serovars recovered were S. Dublin from hide and carcasses and S. Braenderup in ground beef. All isolates were susceptible to 13 anti-microbials. The study highlights that Salmonella can be found at low levels at all stages of beef chain production, processing and retail and that there is a need for multiple hurdle interventions and practices along the beef chain, which will reduce consumer exposure to this pathogen.

Substantial within-animal diversity of Salmonella isolates from lymph nodes, feces, and hides of cattle at slaughter

Lymph nodes (mandibular, mesenteric, mediastinal, and subiliac; n = 68) and fecal (n = 68) and hide (n = 35) samples were collected from beef carcasses harvested in an abattoir in Mexico. Samples were analyzed for Salmonella, and presumptive colonies were subjected to latex agglutination. Of the isolates recovered, a subset of 91 was characterized by serotyping, pulsed-field gel electrophoresis (PFGE), and antimicrobial susceptibility phenotyping. Salmonella was isolated from 100% (hide), 94.1% (feces), 91.2% (mesenteric), 76.5% (subiliac), 55.9% (mandibular), and 7.4% (mediastinal) of samples. From the 87 typeable isolates, eight Salmonella enterica serotypes, including Kentucky (32.2%), Anatum (29.9%), Reading (17.2%), Meleagridis (12.6%), Cerro (4.6%), Muenster (1.1%), Give (1.1%), and Mbandaka (1.1%), were identified. S. Meleagridis was more likely (P = 0.03) to be recovered from lymph nodes than from feces or hides, whereas S. Kentucky was more likely (P = 0.02) to be recovered from feces and hides than from lymph nodes. The majority (59.3%) of the Salmonella isolates were pansusceptible; however, multidrug resistance was observed in 13.2% of isolates. Typing by PFGE revealed that Salmonella strains generally clustered by serotype, but some serotypes (Anatum, Kentucky, Meleagridis, and Reading) were comprised of multiple PFGE subtypes. Indistinguishable PFGE subtypes and, therefore, serotypes were isolated from multiple sample types, and multiple PFGE subtypes were commonly observed within an animal. Given the overrepresentation of some serotypes within lymph nodes, we hypothesize that certain Salmonella strains may be better at entering the bovine host than other Salmonella strains or that some may be better adapted for survival within lymph nodes. Our data provide insight into the ecology of Salmonella within cohorts of cattle and offer direction for intervention opportunities.

Development of a transdermal Salmonella challenge model in calves

Recent investigations have found that Salmonella can be routinely recovered from peripheral lymph nodes (PLNs) of cattle presented for harvest. When contained within the PLNs, this foodborne pathogen is protected from currently used postharvest, inplant intervention strategies and, therefore, PLNs harboring Salmonella may be a potential contaminant of ground beef. The objective of this work was to develop a challenge model that effectively and repeatedly results in Salmonella -positive PLNs. A 10-lancet skin-allergy instrument was inoculated with Salmonella, and calves were inoculated intra- and/or transdermally by applying the device over various ventral regions of the skin. Salmonella was successfully and predictably recovered from regionspecific PLNs up to 8 days postchallenge. Furthermore, serotypes inoculated within specific regions were only recovered from the PLNs draining those regions. This model provides a method to predictably infect PLNs with Salmonella. Further, this model makes it possible to determine the duration of infection and to evaluate candidate interventions that may shorten the duration of infection.

Diversity of pulsed-field gel electrophoresis pulsotypes, serovars, and antibiotic resistance among Salmonella isolates from wild amphibians and reptiles in the California Central Coast

A survey of cold-blooded vertebrates and associated surface waters in a produce-growing region on the Central California Coast was done between May and September 2011 to determine the diversity of Salmonella. Samples from 460 amphibians and reptiles and 119 water samples were collected and cultured for Salmonella. Animals sampled were frogs (n=331), lizards (n=59), newts (n=5), salamanders (n=6), snakes (n=39), and toads (n=20). Salmonella was isolated from 37 individual animals, including frogs, lizards, snakes, and toads. Snakes were the most likely to contain Salmonella, with 59% testing positive followed by 15.3% of lizards, 5% of toads, and 1.2% of frogs. Fifteen water samples (12.6%) were positive. Twenty-two different serovars were identified, and the majority of isolates were S. enterica subsp. IIIb, with subsp. I, II, and IIIa also found. The serovar isolated most frequently was S. enterica subsp. IIIb 16:z₁₀:e,n,x,z₁₅, from snakes and frogs in five different locations. S. enterica subsp. I serovar Typhimurium and the monophasic I 6,8:d:- were isolated from water, and subspecies I Duisburg and its variants were found in animals and water. Some samples contained more than one type of Salmonella. Analysis of pulsed-field gel electrophoresis pulsotypes indicated that some strains persisted in animals and water collected from the same location. Sixty-six isolates displayed antibiotic resistance, with 27 isolates resistant to more than one antibiotic, including a subspecies IIIb isolate from snake having resistance to five different antibiotics. Twenty-three isolates were resistant to more than one class of antibiotic, and six isolates were resistant to three classes. While these subspecies of IIIa and IIIb cause fewer instances of human illness, they may serve as reservoirs of antibiotic resistance, determinants in the environment, and be sources of contamination of leafy greens associated with product recalls.

Microfluidic chip-based detection and intraspecies strain discrimination of Salmonella serovars derived from whole blood of septic mice

Salmonella is a zoonotic pathogen that poses a considerable public health and economic burden in the United States and worldwide. Resultant human diseases range from enterocolitis to bacteremia to sepsis and are acutely dependent on the particular serovar of Salmonella enterica subsp. enterica, which comprises over 99% of human-pathogenic S. enterica isolates. Point-of-care methods for detection and strain discrimination of Salmonella serovars would thus have considerable benefit to medical, veterinary, and field applications that safeguard public health and reduce industry-associated losses. Here we describe a single, disposable microfluidic chip that supports isothermal amplification and sequence-specific detection and discrimination of Salmonella serovars derived from whole blood of septic mice. The integrated microfluidic electrochemical DNA (IMED) chip consists of an amplification chamber that supports loop-mediated isothermal amplification (LAMP), a rapid, single-temperature amplification method as an alternative to PCR that offers advantages in terms of sensitivity, reaction speed, and amplicon yield. The amplification chamber is connected via a microchannel to a detection chamber containing a reagentless, multiplexed (here biplex) sensing array for sequence-specific electrochemical DNA (E-DNA) detection of the LAMP products. Validation of the IMED device was assessed by the detection and discrimination of S. enterica subsp. enterica serovars Typhimurium and Choleraesuis, the causative agents of enterocolitis and sepsis in humans, respectively. IMED chips conferred rapid (under 2 h) detection and discrimination of these strains at clinically relevant levels (<1,000 CFU/ml) from whole, unprocessed blood collected from septic animals. The IMED-based chip assay shows considerable promise as a rapid, inexpensive, and portable point-of-care diagnostic platform for the detection and strain-specific discrimination of microbial pathogens.

Rise of the microbes

Infectious diseases continue to plague the modern world. In the evolutionary arms race of pathogen emergence, the rules of engagement appear to have suddenly changed. Human activities have collided with nature to hasten the emergence of more potent pathogens from natural microbial populations. This is evident in recent infectious disease outbreaks, the events that led to their origin, and lessons learned: influenza (2009), meningitis (Africa, 2009), cholera (Haiti, 2010), E. coli (Germany, 2011) and Salmonella (USA, 2012). Developing a comprehensive control plan requires an understanding of the genetics, epidemiology and evolution of emergent pathogens for which humans have little or no pre-existing immunity. As we plot our next move, nature's genetic lottery continues, providing the fuel to transform the most unlikely infectious disease scenarios into reality.

Distribution and quantification of antibiotic resistant genes and bacteria across agricultural and non-agricultural metagenomes

There is concern that antibiotic resistance can potentially be transferred from animals to humans through the food chain. The relationship between specific antibiotic resistant bacteria and the genes they carry remains to be described. Few details are known about the ecology of antibiotic resistant genes and bacteria in food production systems, or how antibiotic resistance genes in food animals compare to antibiotic resistance genes in other ecosystems. Here we report the distribution of antibiotic resistant genes in publicly available agricultural and non-agricultural metagenomic samples and identify which bacteria are likely to be carrying those genes. Antibiotic resistance, as coded for in the genes used in this study, is a process that was associated with all natural, agricultural, and human-impacted ecosystems examined, with between 0.7 to 4.4% of all classified genes in each habitat coding for resistance to antibiotic and toxic compounds (RATC). Agricultural, human, and coastal-marine metagenomes have characteristic distributions of antibiotic resistance genes, and different bacteria that carry the genes. There is a larger percentage of the total genome associated with antibiotic resistance in gastrointestinal-associated and agricultural metagenomes compared to marine and Antarctic samples. Since antibiotic resistance genes are a natural part of both human-impacted and pristine habitats, presence of these resistance genes in any specific habitat is therefore not sufficient to indicate or determine impact of anthropogenic antibiotic use. We recommend that baseline studies and control samples be taken in order to determine natural background levels of antibiotic resistant bacteria and/or antibiotic resistance genes when investigating the impacts of veterinary use of antibiotics on human health. We raise questions regarding whether the underlying biology of each type of bacteria contributes to the likelihood of transfer via the food chain.

Efficacy of chemical interventions against Escherichia coli O157:H7 and multidrug-resistant and antibiotic-susceptible Salmonella on inoculated beef trimmings

Studies were conducted to compare the decontamination efficacy of six chemical treatments against Escherichia coli O157:H7 and multidrug-resistant and antibiotic-susceptible Salmonella inoculated on beef trimmings. The inocula, comprising four-strain mixtures of rifampin-resistant E. coli O157:H7 and antibiotic-susceptible or multidrug-resistant (MDR and/or MDR-AmpC) Salmonella Newport and Salmonella Typhimurium, were inoculated (3 log CFU/cm(2)) separately onto samples (10 by 5 by 1 cm) derived from beef chuck rolls. Samples were left untreated (control), were immersed for 30 s in acidified sodium chlorite (0.1%, pH 2.5), peroxyacetic acid (0.02%, pH 3.8), sodium metasilicate (4%, pH 12.6), Bromitize Plus (0.0225% active bromine, pH 6.6), or AFTEC 3000 (pH 1.2), or were immersed for 5 s in SYNTRx 3300 (pH 1.0). Levels of surviving Salmonella on treated trimmings were not influenced by serotype or antibiotic resistance phenotype and were generally similar (P ≥ 0.05) or lower (P < 0.05) than levels of surviving E. coli O157:H7 regardless of antimicrobial treatment. Overall, depending on chemical treatment (reductions within each chemical treatment were similar among all tested inocula), initial counts of E. coli O157:H7 (2.7 to 3.1 log CFU/cm(2)) were reduced (P < 0.05) by 0.2 to 1.4 log CFU/cm(2). Similarly, initial counts of the tested Salmonella inocula (2.8 to 3.3 log CFU/cm(2)) were reduced (P < 0.05) by 0.4 to 1.4 (Salmonella Newport, antibiotic susceptible), 0.3 to 1.4 (Salmonella Newport, MDR-AmpC), 0.2 to 1.5 (Salmonella Typhimurium, antibiotic susceptible), 0.4 to 1.3 (Salmonella Typhimurium, MDR), and 0.4 to 1.5 (Salmonella Typhimurium, MDR-AmpC) log CFU/cm(2), depending on antimicrobial treatment. Reductions obtained with sodium metasilicate were 1.3 to 1.5 log CFU/cm(2), regardless of inoculum, and reductions obtained with the five remaining antimicrobial treatments were 0.2 to 0.7 log CFU/cm(2) (depending on treatment). Findings of this study should be useful to regulatory authorities and the meat industry as they consider Salmonella contamination on beef trimmings.