Antimicrobial use and resistance in animals

Escherichia coli isolates from sick chickens in China: changes in antimicrobial resistance between 1993 and 2013

The use of antimicrobials for the control of infectious disease has increased in recent decades. Understanding trends in antimicrobial resistance provides clues about the relationship between antimicrobial use and the emergence of resistance. We examined the resistance of 540 Escherichia coli isolates to 19 antimicrobials that represent 11 classes of antimicrobial agents. The isolates were collected from chickens between 1993 and 2013 in China. Overall, >96.7% of the isolates were resistant to at least one of the tested compounds, and 87.2% of them displayed multidrug resistance (MDR) representing five to six antimicrobial classes. A high proportion of E. coli isolates were resistant to tetracycline (90.6%), nalidixic acid (80.6%), ampicillin (77.2%), trimethoprim-sulfamethoxazole (76.9%), and streptomycin (72.8%). Only 3.0% of the isolates were resistant to nitrofurantoin, and none was resistant to meropenem. Resistance to amikacin, ampicillin, aztreonam, ceftazidime, cefotaxime, cephalothin, chloramphenicol, ciprofloxacin, fosfomycin, levofloxacin, norfloxacin, nalidixic acid, piperacillin, and trimethoprim-sulfamethoxazole significantly increased from 1993 to 2013 (P <0.01). There was an increasing trend in MDR over the 20 year period.

Antimicrobial Activity of Selected Phytochemicals against Escherichia coli and Staphylococcus aureus and Their Biofilms

Abstract Bacteria can be resistant to multiple antibiotics and we are fast approaching a time when antibiotics will not work on some bacterial infections. New antimicrobial compounds are urgently necessary. Plants are considered the greatest source to obtain new antimicrobials. This study aimed to assess the antimicrobial activity of four phytochemicals—7-hydroxycoumarin (7-HC), indole-3-carbinol (I3C), salicylic acid (SA) and saponin (SP)—against Escherichia coli and Staphylococcus aureus, either as planktonic cells or as biofilms. These bacteria are commonly found in hospital-acquired infections. Some aspects on the phytochemicals mode of action, including surface charge, hydrophobicity, motility and quorum-sensing inhibition (QSI) were investigated. In addition, the phytochemicals were combined with three antibiotics in order to assess any synergistic effect. 7-HC and I3C were the most effective phytochemicals against E. coli and S. aureus. Both phytochemicals affected the motility and quorum-sensing (QS) activity, which means that they can play an important role in the interference of cell-cell interactions and in biofilm formation and control. However, total biofilm removal was not achieved with any of the selected phytochemicals. Dual combinations between tetracycline (TET), erythromycin (ERY) and ciprofloxacin (CIP) and I3C produced synergistic effects against S. aureus resistant strains. The overall results demonstrates the potential of phytochemicals to control the growth of E. coli and S. aureus in both planktonic and biofilm states. In addition, the phytochemicals demonstrated the potential to act synergistically with antibiotics, contributing to the recycling of old antibiotics that were once considered ineffective due to resistance problems.

Review: Chinese herbs as alternatives to antibiotics in feed for swine and poultry production: Potential and challenges in application

Gong, J., Yin, F., Hou, Y. and Yin, Y. 2014. Chinese herbs as alternatives to antibiotics in feed for swine and poultry production: Potential and challenges in application. Can. J. Anim. Sci. 94: 223–241. Traditional Chinese medicine (TCM) has a long history of clinical practice, and its own theoretical framework focused on functions at the whole-body level. However, due to cultural differences, TCM has not been fully recognized in Western countries. With the recent development of the theory of whole-body systems biology and “-omics”, there is a new opportunity to study TCM and to close the gap between TCM and Western medicine, because of the similarity in the theoretical foundations between TCM and whole-body systems biology. The uniqueness of TCM theory and practice is the approach to maintain and restore the body balance as a whole with no or little unfavourable side effects. Recent studies have also shown that Chinese herbs used as feed additives can modulate nutritional metabolism, immune responses, and intestinal health of food-producing animals, demonstrating good potential as substitutes for dietary antibiotics. Nonetheless, some issues need to be addressed before Chinese herbs can reach their full application. This article has critically reviewed recent progresses in scientific research of Chinese herbs as feed additives and their potential to replace dietary antibiotics. Possible challenges in future application for swine and poultry production are also discussed.

Effects of dietary supplementation of quercetin on performance, egg quality, cecal microflora populations, and antioxidant status in laying hens

Plant polyphenols, especially flavonoids, are of great interest due to their wide range of biological activities. Quercetin, a ubiquitous flavonoid, is known to have antioxidant and antibacterial effects. In this study, we investigated the effect of quercetin on performance, egg quality, cecal microflora populations, and antioxidant status in laying hens. Two hundred forty 28-wk-old Hessian laying hens, with an average laying rate of lay 85% at the start, were randomly allotted to 4 treatments and fed 1 of 4 diets (negative control, 0.2, 0.4, and 0.6 g of quercetin/kg of diet) for 8 wk. Layer performance responses, egg quality parameters, cecal microflora populations and antioxidant status were measured at the end of the experiment. Results showed that feed conversion decreased as the quercetin level increased. Laying rate had a quadratic correlation with the level of quercetin (P = 0.056) and was maximized by the supplementation level of 0.2 g/kg of diet. However, no significant quercetin effect was observed on egg quality. Regression analysis showed that the population of total aerobes and coliforms decreased and the population of Bifidobacteria increased as the level of quercetin increased. Regression analysis also showed the activities of Cu-Zn-superoxide dismutase increased as the level of quercetin increased (P < 0.05). Results of the study suggest that the appropriate level of supplementation is 0.367 to 0.369 g of quercetin/kg of feed based on the improvement of laying rate (with 88.55 as maximum value) and feed conversion (with 2.0725 as minimum value). Our observations provided further evidence that dietary supplementation of quercetin improved performance by modulation of intestinal environment and liver superoxide dismutase content in laying hens. Quercetin has the potential as functional feed additive in animal production.

Unravelling a vicious circle: animal feed marketed in Costa Rica contains irregular concentrations of tetracyclines and abundant oxytetracycline-resistant Gram-positive bacteria

Diverse tetracyclines are used to prevent and control bacterial infections in livestock and farmed fish. These drugs are administered through the diet, but farmers seldom check whether feed contains antibiotic-resistant bacteria that may colonise their crops or transfer their resistance traits to species of veterinary relevance. To examine whether antibiotic dosage defines the abundance of antibiotic-resistant bacteria in animal feed, we determined the concentration of parental compounds and epimers of oxytetracycline (OTC), doxycycline, tetracycline and chlortetracycline, as well as the abundance and resistance level of OTC-resistant bacteria in samples of fish (n = 21), poultry (n = 21), swine (n = 21), and shrimp feed (n = 21) marketed in Costa Rica. Fish feed contained the highest amounts of tetracyclines (119-8365 mg kg(-1)) and the largest proportion of bacteria resistant to 10 μg ml(-1) (1.8-92.4%) or 100 μg ml(-1) of OTC (12.5-63.8%). Poultry (78-438 mg kg(-1)) and swine (41-1076 mg kg(-1)) feed had intermediate concentrations of tetracyclines and OTC-resistant bacteria (0.2-66% and 0.3-49%, respectively), whereas shrimp feed showed the lowest amounts of tetracyclines (21.5-50.3 mg kg(-1)), no OTC and no culturable OTC-resistant bacteria. In line with these results, the MIC50 of OTC for 150 isolates from fish and poultry feed was > 256 µg ml(-1), while that of 150 bacteria isolated from swine feed was 192 µg ml(-1). Phenotypic tests, fatty acid profiles and proteotypic analyses by matrix-assisted laser desorption/ionisation-time of flight mass-spectroscopy revealed that most OTC-resistant isolates were Gram-positive bacteria of low G+C% content from the genera Staphylococcus and Bacillus. Clear correlations between OTC dosage and feed colonisation with OTC-resistant bacteria were seen in medicated feed for fish (r = 0.179-0.651). Nonetheless, some unmedicated feed for fish, swine and poultry contained large populations of OTC-resistant bacteria, suggesting that raw materials and manufacturing processes may also influence carriage of OTC-resistant bacteria in animal feed.

Latent class comparison of test accuracy when evaluating antimicrobial susceptibility using disk diffusion and broth microdilution to testEscherichia coliandMannheimia haemolyticaisolates recovered from beef feedlot cattle

The study objective was to use Bayesian latent class analysis to evaluate the accuracy of susceptibility test results obtained from disk diffusion and broth microdilution using bacteria recovered from beef feedlot cattle. Isolates ofEscherichia coliandMannheimia haemolyticawere tested for susceptibility to ampicillin, ceftiofur, streptomycin, sulfisoxazole, tetracycline, and trimethoprim-sulfamethoxazole. Results showed that neither testing method was always or even generally superior to the other. Specificity (ability to correctly classify non-resistant isolates) was extremely high for both testing methods, but sensitivity (ability to correctly classify resistant isolates) was lower, variable in the drugs evaluated, and variable between the two bacterial species. Predictive values estimated using Bayesian Markov chain Monte Carlo models showed that the ability to predict true susceptibility status was equivalent for test results obtained with the two testing methods for some drugs, but for others there were marked differences between results obtained from disk diffusion and broth microdilution tests.

A unique megaplasmid contributes to stress tolerance and pathogenicity of an emergent Salmonella enterica serovar Infantis strain

Of all known Salmonella enterica serovars, S. Infantis is one of the most commonly isolated and has been recently emerging worldwide. To understand the recent emergence of S. Infantis in Israel, we performed extensive comparative analyses between pre-emergent and the clonal emergent S. Infantis populations. We demonstrate the fixation of adaptive mutations in the DNA gyrase (gyrA) and nitroreductase (nfsA) genes, conferring resistance to quinolones and nitrofurans, respectively, and the carriage of an emergent-specific plasmid, designated pESI. This self-transferred episome is a mosaic megaplasmid (∼280 kb), which increases bacterial tolerance to environmental mercury (mer operon) and oxidative stress, and provides further resistance to tetracycline, sulfamethoxazole and trimethoprim, most likely due to the presence of tetRA, sulI and dfrA genes respectively. Moreover, pESI carries the yersiniabactin siderophore system and two novel chaperone-usher fimbriae. In vitro studies established that pESI conjugation into a plasmidless S. Infantis strain results in superior biofilm formation, adhesion and invasion into avian and mammalian host cells. In vivo mouse infections demonstrated higher pathogenicity and increased intestinal inflammation caused by an S. Infantis strain harboring pESI compared with the plasmidless parental strain. Our results indicate that the presence of pESI that was found only in the emergent population of S. Infantis in Israel contributes significantly to antimicrobials tolerance and pathogenicity of its carrier. It is highly likely that pESI plays a key role in the successful spread of the emergent clone that replaced the local S. Infantis community in the short time of only 2-3 years.

In vivo spread of macrolide-lincosamide-streptogramin B (MLSB) resistance--a model study in chickens

The influence of specific and non-specific antibiotic pressure on in vivo spread of macrolide-lincosamide-streptogramin B (MLSB) resistance was evaluated in this study. Chickens repeatedly inoculated with Enterococcus faecalis harbouring the plasmid pAMβ1 carrying the erm(B) gene were perorally treated for one week with tylosin, lincomycin (both specific antibiotic pressure) and chlortetracycline (non-specific antibiotic pressure). Antibiotic non-treated but E. faecalis inoculated chickens served as a control. To quantify the erm(B) gene and characterise intestinal microflora, faecal DNA was analysed by qPCR and 454-pyrosequencing. Under the pressure of antibiotics, a significant increase in erm(B) was observed by qPCR. However, at the final stage of the experiment, an increase in erm(B) was also observed in two out of five non-treated chickens. In chickens treated with tylosin and chlortetracycline, the increase in erm(B) was accompanied by an increase in enterococci. However, E. faecalis was at the limit of detection in all animals. This suggests that the erm(B) gene spread among the gut microbiota other than E. faecalis. Pyrosequencing results indicated that, depending on the particular antibiotic pressure, different bacteria could be responsible for the spread of MLSB resistance. Different species of MLSB-resistant enterococci and streptococci were isolated from cloacal swabs during and after the treatment. PFGE analysis of MLSB-resistant enterococci revealed four clones, all differing from the challenge strain. All of the MLSB-resistant isolates harboured a plasmid of the same size as pAMβ1. This study has shown that MLSB resistance may spread within the gut microbiota under specific and non-specific pressure and even in the absence of any antimicrobial pressure. Finally, depending on the particular antibiotic pressure, different bacterial species seems to be involved in the spread of MLSB resistance.

Report of ribosomal RNA methylase gene erm(B) in multidrug-resistant Campylobacter coli

OBJECTIVES

Campylobacter is a major foodborne enteric pathogen and macrolides are the drug of choice for the clinical therapy of campylobacteriosis. Macrolide resistance among Campylobacter compromises clinical treatment, is associated with adverse health events and is a significant public health concern. Here, we report the first identification of a horizontally transferrable macrolide resistance mechanism in porcine Campylobacter coli ZC113 that is mediated by a ribosomal RNA methylase, Erm(B).

METHODS

Horizontal transfer of a macrolide resistance determinant between C. coli and Campylobacter jejuni was performed by natural transformation. Whole-genome sequencing was initially used to identify the ribosomal methylase-encoding gene erm(B) in Campylobacter. Cloning of erm(B) into C. jejuni NCTC 11168 was performed to evaluate whether the erm(B) gene is responsible for high-level macrolide resistance in Campylobacter.

RESULTS

The erm(B) gene was identified in ZC113, conferred high-level resistance to macrolides and was associated with a chromosomal multidrug-resistant genomic island (MDRGI). The MDRGI probably originated from Gram-positive bacteria and was horizontally transferred between C. coli and C. jejuni via natural transformation. Furthermore, the erm(B)-positive isolate ZC113 was resistant to all clinically important antibiotics used for treating campylobacteriosis and is essentially multidrug-resistant Campylobacter.

CONCLUSIONS

To the best of our knowledge, this is the first report of a horizontally transferable macrolide resistance mechanism in thermophilic Campylobacter. Surveillance of erm(B) and its associated MDRGI in both C. coli and C. jejuni is urgently warranted.

Molecular characterization of Salmonella enterica serovar Typhimurium isolated from human, food, and animal sources in Malaysia

Salmonella Typhimurium is an important nontyphoidal Salmonella serovar associated with foodborne diseases in many parts of the world. This organism is the major causative agent of nontyphoidal salmonellosis in Malaysia. We aimed to investigate the genetic profiles of the strains isolated from clinical, zoonotic, and dietary sources in Malaysia using multilocus variable number tandem repeat analysis (MLVA) and pulsed-field gel electrophoresis (PFGE). By focusing on the 5 common variable number tandem repeat (VNTR) loci, we found that PFGE (D = 0.99) was more discriminative than MLVA (D = 0.76). The low MLVA score might be because of a lack of VNTR loci STTR6 (81.0%) and STTR10pl (76.2%). Both subtyping methods suggested that our S. Typhimurium strains were largely endemic with limited genetic variation. Furthermore, we observed that biphasic S. Typhimurium strains were dominant (99%) and multidrug resistance was prevalent (50%) within our sample pool. The most frequently observed phenotypes were resistance to compound sulfonamides (49%), tetracycline (51%), and streptomycin (52%). In this study, we documented the genetic relationship, antimicrobial resistance characteristics, and flagellar-phase dominance among S. Typhimurium strains found in Malaysia.

Describing antimicrobial use and reported treatment efficacy in Ontario swine using the Ontario Swine Veterinary-based Surveillance program

Background

The objective of this work was to retrospectively assess records received through the Ontario Swine Veterinary-based Surveillance program July 2007 – July 2009 to describe and assess relationships between reported treatment failure, antimicrobial use, diagnosis and body system affected.

Results

Antimicrobial use occurred in 676 records, 80.4% of all records recording treatment (840). The most commonly used antimicrobials were penicillin (34.9%), tetracyclines (10.7%) and ceftiofur (7.8%), and the use of multiple antimicrobials occurred in 141/676 records (20.9%). A multi-level logistic regression model was built to describe the probability of reported treatment failure. The odds of reported treatment failure were significantly reduced if the record indicated that the gastro-intestinal (GI) system was affected, as compared to all other body systems (p < 0.05). In contrast, the odds of reported treatment failure increased by 1.98 times if two antimicrobials were used as compared to one antimicrobial (p = 0.009) and by 6.52 times if three or more antimicrobials were used as compared to one antimicrobial (p = 0.005). No significant increase in reported treatment failure was seen between the use of two antimicrobials and three or more antimicrobials. No other antimicrobials were significantly associated with reported treatment failure after controlling for body system and the number of antimicrobials used.

Conclusions

Failure of antimicrobial treatment is more likely to occur in non-GI conditions, as compared to GI conditions and the use of multiple antimicrobial products is also associated with an increased probability of antimicrobial treatment failure. The authors suggest that a more preventative approach to herd health should be taken in order to reduce antimicrobial inputs on-farm, including improved immunity via vaccination, management and biosecurity strategies. Furthermore, improved immunity may be viewed as a form of antimicrobial stewardship to the industry by reducing required antimicrobial inputs and consequently, reduced selection pressure for AMR.

Occurrence, serotype diversity, and antimicrobial resistance of salmonella in ground beef at retail stores in Jalisco state, Mexico

The occurrence, serotype diversity, and antimicrobial resistance of Salmonella bacteria in commercial ground beef at retail establishments were investigated. Salmonella was isolated from 135 (56.7%) of 238 ground beef samples collected at the same number of butcher's shops located in three municipalities of Jalisco State, Mexico, during an 11-month period. The isolation frequency differed by municipality (P < 0.05) and was higher (P < 0.05) during the warm season (68.5%) than during the cold season (43.2%). Overall, 25 serotypes and 8 serogroups were identified among 135 Salmonella isolates; predominant were Salmonella group B (9.6%), Salmonella Anatum (8.9%), Salmonella Agona (6.7%), Salmonella Infantis (6.7%), and Salmonella Typhimurium (5.9%). All Salmonella isolates were tested for susceptibility to 11 antimicrobial drugs of human and veterinary use. Resistance to tetracycline was the most commonly observed (40.7%), followed by resistance to streptomycin (35.6%), trimethoprim-sulfamethoxazole (20.7%), and nalidixic acid (19.3%). Thirty-seven Salmonella isolates (27.4%) were multidrug resistant, and the majority corresponded to Salmonella Group B, Salmonella Anatum, and Salmonella Typhimurium. Three Salmonella isolates were resistant to seven different antimicrobials. The frequency of Salmonella in ground beef samples (56.7%) was higher than that observed in our previous investigation on beef carcasses (15.4%) at small abattoirs in the same region of Mexico. This may be a result of increasing contamination at these two points of the raw-beef production chain or may be an effect of the grinding process that facilitates a more-homogeneous pathogen distribution in the product. Poor hygiene, temperature abuse, and practices allowing cross-contamination during ground beef fabrication at these retail establishments increase the consumer's exposure to Salmonella.

Pathogens of bovine respiratory disease in North American feedlots conferring multidrug resistance via integrative conjugative elements

In this study, we determined the prevalence of bovine respiratory disease (BRD)-associated viral and bacterial pathogens in cattle and characterized the genetic profiles, antimicrobial susceptibilities, and nature of antimicrobial resistance determinants in collected bacteria. Nasopharyngeal swab and lung tissue samples from 68 BRD mortalities in Alberta, Canada (n = 42), Texas (n = 6), and Nebraska (n = 20) were screened using PCR for bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus, bovine herpesvirus 1, parainfluenza type 3 virus, Mycoplasma bovis, Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni. Excepting bovine herpesvirus 1, all agents were detected. M. haemolytica (91%) and BVDV (69%) were the most prevalent, with cooccurrence in 63% of the cattle. Isolates of M. haemolytica (n = 55), P. multocida (n = 8), and H. somni (n = 10) from lungs were also collected. Among M. haemolytica isolates, a clonal subpopulation (n = 8) was obtained from a Nebraskan feedlot. All three bacterial pathogens exhibited a high rate of antimicrobial resistance, with 45% exhibiting resistance to three or more antimicrobials. M. haemolytica (n = 18), P. multocida (n = 3), and H. somni (n = 3) from Texas and Nebraska possessed integrative conjugative elements (ICE) that conferred resistance for up to seven different antimicrobial classes. ICE were shown to be transferred via conjugation from P. multocida to Escherichia coli and from M. haemolytica and H. somni to P. multocida. ICE-mediated multidrug-resistant profiles of bacterial BRD pathogens could be a major detriment to many of the therapeutic antimicrobial strategies currently used to control BRD.

Methodological comparisons for antimicrobial resistance surveillance in feedlot cattle

BACKGROUND

The purpose of this study was to objectively compare methodological approaches that might be utilized in designing an antimicrobial resistance (AMR) surveillance program in beef feedlot cattle. Specifically, four separate comparisons were made to investigate their potential impact on estimates for prevalence of AMR. These included investigating potential differences between 2 different susceptibility testing methods (broth microdilution and disc diffusion), between 2 different target bacteria (non-type-specific E. coli [NTSEC] and Mannheimia haemolytica), between 2 strategies for sampling feces (individual samples collected per rectum and pooled samples collected from the pen floor), and between 2 strategies for determining which cattle to sample (cattle that were culture-positive for Mannheimia haemolytica and those that were culture-negative).

RESULTS

Comparing two susceptibility testing methods demonstrated differences in the likelihood of detecting resistance between automated disk diffusion (BioMIC®) and broth microdilution (Sensititre®) for both E. coli and M. haemolytica. Differences were also detected when comparing resistance between two bacterial organisms within the same cattle; there was a higher likelihood of detecting resistance in E. coli than in M. haemolytica. Differences in resistance prevalence were not detected when using individual animal or composite pen sampling strategies. No differences in resistance prevalences were detected in E. coli recovered from cattle that were culture-positive for M. haemolytica compared to those that were culture-negative, suggesting that sampling strategies which targeted recovery of E. coli from M. haemolytica-positive cattle would not provide biased results.

CONCLUSIONS

We found that for general purposes, the susceptibility test selected for AMR surveillance must be carefully chosen considering the purpose of the surveillance since the ability to detect resistance appears to vary between these tests depending upon the population where they are applied. Continued surveillance of AMR in M. haemolytica recovered by nasopharyngeal swab is recommended if monitoring an animal health pathogen is an objective of the surveillance program as results of surveillance using fecal E. coli cannot be extrapolated to this important respiratory pathogen. If surveillance of E. coli was pursued in the same population, study populations could target animals that were culture-positive for M. haemolytica without biasing estimates for AMR in E. coli. Composite pen-floor sampling or sampling of individuals per-rectum could possibly be used interchangeably for monitoring resistance in E. coli.

Animal husbandry practices in rural Bangladesh: potential risk factors for antimicrobial drug resistance and emerging diseases

Antimicrobial drug administration to household livestock may put humans and animals at risk for acquisition of antimicrobial drug-resistant pathogens. To describe animal husbandry practices, including animal healthcare-seeking and antimicrobial drug use in rural Bangladesh, we conducted semi-structured in-depth interviews with key informants, including female household members (n = 79), village doctors (n = 10), and pharmaceutical representatives, veterinarians, and government officials (n = 27), and performed observations at animal health clinics (n = 3). Prevalent animal husbandry practices that may put persons at risk for acquisition of pathogens included shared housing and water for animals and humans, antimicrobial drug use for humans and animals, and crowding. Household members reported seeking human and animal healthcare from unlicensed village doctors rather than formal-sector healthcare providers and cited cost and convenience as reasons. Five times more per household was spent on animal than on human healthcare. Strengthening animal and human disease surveillance systems should be continued. Interventions are recommended to provide vulnerable populations with a means of protecting their livelihood and health.

Considerations on the aquaculture development and on the use of veterinary drugs: special issue for fluoroquinolones--a review

Aquaculture has become an important source of fish available for human consumption. In order to achieve greater productivity, intensive fish cultivation systems are employed, which can cause greater susceptibility to diseases caused by viruses, bacteria, fungi, and parasites. Antimicrobial substances are compounds used in livestock production with the objectives of inhibiting the growth of microorganisms and treatment or prevention of diseases. It is well recognized that the issues of antimicrobial use in food animals are of global concern about its impact on food safety. This paper present an overview of the aquaculture production in the whole world, raising the particularities in Brazil, highlighting the importance of the use of veterinary drugs in this system of animal food production, and address the potential risks arising from their indiscriminate use and their impacts on aquaculture production as they affect human health and the environment. The manuscript also discusses the analytical methods commonly used in the determination of veterinary drug residues in fish, with special issue for fluroquinolones residues and with emphasis on employment of LC-MS/MS analytical technique.

Longitudinal study of distributions of similar antimicrobial-resistant Salmonella serovars in pigs and their environment in two distinct swine production systems

The aim of this longitudinal study was to determine and compare the prevalences and genotypic profiles of antimicrobial-resistant (AR) Salmonella isolates from pigs reared in antimicrobial-free (ABF) and conventional production systems at farm, at slaughter, and in their environment. We collected 2,889 pig fecal and 2,122 environmental (feed, water, soil, lagoon, truck, and floor swabs) samples from 10 conventional and eight ABF longitudinal cohorts at different stages of production (farrowing, nursery, finishing) and slaughter (postevisceration, postchill, and mesenteric lymph nodes [MLN]). In addition, we collected 1,363 carcass swabs and 205 lairage and truck samples at slaughter. A total of 1,090 Salmonella isolates were recovered from the samples; these were isolated with a significantly higher prevalence in conventionally reared pigs (4.0%; n = 66) and their environment (11.7%; n = 156) than in ABF pigs (0.2%; n = 2) and their environment (0.6%; n = 5) (P < 0.001). Salmonella was isolated from all stages at slaughter, including the postchill step, in the two production systems. Salmonella prevalence was significantly higher in MLN extracted from conventional carcasses than those extracted from ABF carcasses (P < 0.001). We identified a total of 24 different serotypes, with Salmonella enterica serovar Typhimurium, Salmonella enterica serovar Anatum, Salmonella enterica serovar Infantis, and Salmonella enterica serovar Derby being predominant. The highest frequencies of antimicrobial resistance (AR) were exhibited to tetracycline (71%), sulfisoxazole (42%), and streptomycin (17%). Multidrug resistance (resistance to ≥ 3 antimicrobials; MDR) was detected in 27% (n = 254) of the Salmonella isolates from the conventional system. Our study reports a low prevalence of Salmonella in both production systems in pigs on farms, while a higher prevalence was detected among the carcasses at slaughter. The dynamics of Salmonella prevalence in pigs and carcasses were reciprocated in the farm and slaughter environment, clearly indicating an exchange of this pathogen between the pigs and their surroundings. Furthermore, the phenotypic and genotypic fingerprint profile results underscore the potential role played by environmental factors in dissemination of AR Salmonella to pigs.

Effect of subtherapeutic vs. therapeutic administration of macrolides on antimicrobial resistance in Mannheimia haemolytica and enterococci isolated from beef cattle

Macrolides are the first-line treatment against bovine respiratory disease (BRD), and are also used to treat infections in humans. The macrolide, tylosin phosphate, is often included in the diet of cattle as a preventative for liver abscesses in many regions of the world outside of Europe. This study investigated the effects of administering macrolides to beef cattle either systemically through a single subcutaneous injection (therapeutic) or continuously in-feed (subtherapeutic), on the prevalence and antimicrobial resistance of Mannheimia haemolytica and Enterococcus spp. isolated from the nasopharynx and faeces, respectively. Nasopharyngeal and faecal samples were collected weekly over 28 days from untreated beef steers and from steers injected once with tilmicosin or tulathromycin or continuously fed tylosin phosphate at dosages recommended by manufacturers. Tilmicosin and tulathromycin were effective in lowering (P < 0.05) the prevalence of M. haemolytica, whereas subtherapeutic tylosin had no effect. M. haemolytica isolated from control- and macrolide-treated animals were susceptible to macrolides as well as to other antibiotics. Major bacteria co-isolated with M. haemolytica from the nasopharynx included Pasteurella multocida, Staphylococcus spp., Acinetobacter spp., Escherichia coli and Bacillus spp. With the exception of M. haemolytica and P. multocida, erythromycin resistance was frequently found in other isolated species. Both methods of macrolide administration increased (P < 0.05) the proportion of erythromycin resistant enterococci within the population, which was comprised almost exclusively of Enterococcus hirae. Injectable macrolides impacted both respiratory and enteric microbes, whereas orally administered macrolides only influenced enteric bacteria.

Experimental viral evolution reveals major histocompatibility complex polymorphisms as the primary host factors controlling pathogen adaptation and virulence

Using an experimental evolution approach, we recently demonstrated that the mouse-specific pathogen Friend virus (FV) complex adapted to specific major histocompatibility complex (MHC) genotypes, which resulted in fitness tradeoffs when viruses were exposed to hosts possessing novel MHC polymorphisms. Here we report the analysis of patterns of pathogen adaptation and virulence evolution from viruses adapting to one of three hosts that differ across the entire genome (A/WySn, DBA/2J and BALB/c). We found that serial passage of FV complex through these mouse genotypes resulted in significant increases in pathogen fitness (156-fold) and virulence (11-fold). Adaptive responses by post-passage viruses also resulted in host-genotype-specific patterns of adaptation. To evaluate the relative importance of MHC versus non-MHC polymorphisms as factors influencing pathogen adaptation and virulence, we compared the magnitude of fitness tradeoffs incurred by post-passage viruses when infecting hosts possessing either novel MHC polymorphisms alone or hosts possessing novel MHC and non-MHC polymorphisms. MHC polymorphisms alone accounted for 71% and 83% of the total observed reductions in viral fitness and virulence in unfamiliar host genotypes, respectively. Strikingly, these data suggest that genetic polymorphisms within the MHC, a gene region representing only -0.1% of the genome, are major host factors influencing pathogen adaptation and virulence evolution.

Genetic mechanisms of antimicrobial resistance identified in Salmonella enterica, Escherichia coli, and Enteroccocus spp. isolated from U.S. food animals

The prevalence of antimicrobial resistance (AR) in bacteria isolated from U.S. food animals has increased over the last several decades as have concerns of AR foodborne zoonotic human infections. Resistance mechanisms identified in U.S. animal isolates of Salmonella enterica included resistance to aminoglycosides (e.g., alleles of aacC, aadA, aadB, ant, aphA, and StrAB), β-lactams (e.g., bla_{CMY−2, TEM−1, PSE−1}), chloramphenicol (e.g., floR, cmlA, cat1, cat2), folate pathway inhibitors (e.g., alleles of sul and dfr), and tetracycline [e.g., alleles of tet(A), (B), (C), (D), (G), and tetR]. In the U.S., multi-drug resistance (MDR) mechanisms in Salmonella animal isolates were associated with integrons, or mobile genetic elements (MGEs) such as IncA/C plasmids which can be transferred among bacteria. It is thought that AR Salmonella originates in food animals and is transmitted through food to humans. However, some AR Salmonella isolated from humans in the U.S. have different AR elements than those isolated from food animals, suggesting a different etiology for some AR human infections. The AR mechanisms identified in isolates from outside the U.S. are also predominantly different. For example the extended spectrum β-lactamases (ESBLs) are found in human and animal isolates globally; however, in the U.S., ESBLs thus far have only been found in human and not food animal isolates. Commensal bacteria in animals including Escherichia coli and Enterococcus spp. may be reservoirs for AR mechanisms. Many of the AR genes and MGEs found in E. coli isolated from U.S. animals are similar to those found in Salmonella. Enterococcus spp. isolated from animals frequently carry MGEs with AR genes, including resistances to aminoglycosides (e.g., alleles of aac, ant, and aph), macrolides [e.g., erm(A), erm(B), and msrC], and tetracyclines [e.g., tet(K), (L), (M), (O), (S)]. Continuing investigations are required to help understand and mitigate the impact of AR bacteria on human and animal health.

Antimicrobial resistance and prudent drug use forStreptococcus suis

This paper reviews information on antimicrobial resistance patterns and prudent use of antimicrobials to reduce the impact and spread of resistantStreptococcus suisstrains.S. suisis an important pathogen in swine, which can cause significant economic loss. Prudent use of antimicrobials forS. suisis essential to preserve the therapeutic efficacy of broad-spectrum antimicrobials and to minimize selection of resistantS. suisstrains. Resistance ofS. suisto antimicrobials commonly used in swine, including lincosamides, macrolides, sulphonamides, and tetracycline, has been documented worldwide, with resistance in up to 85% of strains. Among antimicrobials examined, resistance ofS. suishas been demonstrated to be relatively low for penicillin (0–27%), ampicillin (0.6–23%), and ceftiofur (0–23%). For penicillin, this result may be due in part to the unique mechanism by which resistance is acquired through modifications in the structure of penicillin-binding proteins. Recommendations to controlS. suisinfection include focused and careful choice and appropriate use of antimicrobials, together with preventive measures intended to improve swine management.

Antimicrobial multidrug resistance and coresistance patterns of Mannheimia haemolytica isolated from bovine respiratory disease cases--a three-year (2009-2011) retrospective analysis

Bovine respiratory disease continues to be the most important ailment of feed yard cattle. While the disease is multifactorial in nature, therapy continues to target the primary bacterial pathogens, Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni. A survey of records from a single diagnostic laboratory was conducted to evaluate the percentage of M. haemolytica isolates that were resistant to multiple antimicrobials and if coresistance patterns could be detected. All susceptibility test results for M. haemolytica recovered from lung tissues of cattle were eligible for inclusion in the survey. There were no isolates over the course of the analysis that were resistant to all 6 antimicrobials, primarily due to a lack of resistance to ceftiofur. In 2009, just over 5% of isolates were resistant to 5 or more antimicrobials (pan-resistant). In 2011, more than 35% of the M. haemolytica isolates were characterized as pan-resistant. Significant antimicrobial coresistance patterns were only seen with oxytetracycline and tilmicosin; bacterial isolates that were resistant to either oxytetracycline or tilmicosin were more likely to be resistant to at least one other antimicrobial. The mechanisms by which M. haemolytica is developing multidrug resistance warrant investigation if antimicrobial utility in the therapy of bovine respiratory disease is to be preserved.

Impact of subtherapeutic administration of tylosin and chlortetracycline on antimicrobial resistance in farrow-to-finish swine

The use of antimicrobial agents in swine production at subtherapeutic concentrations for the purpose of growth promotion remains controversial due to the potential impact on public health. Beginning at weaning (3 weeks), pigs received either nonmedicated feed or feed supplemented with subtherapeutic levels of either tylosin (11-44 ppm) or chlortetracycline (5.5 ppm). After only 3 weeks, pigs given feed supplemented with tylosin had significantly higher levels of tylosin-resistant anaerobes (P < 0.0001) compared with the control group, increasing from 11.8% to 89.6%, a level which was stable for the duration of the study, even after a 2-week withdrawal prior to slaughter. Tylosin-fed pigs had a higher incidence of detection for erm(A), erm(F), and erm(G), as well as significantly (P < 0.001) higher concentrations of erm(B) in their feces. The continuous administration of chlortetracycline-supplemented feed, however, had no significant effect on the population of chlortetracycline-resistant anaerobes in comparison with nontreated pigs (P > 0.05). The resistance genes tet(O), tet(Q), and erm(B) were detected in all pigs at each sampling time, while tet(G), tet(L), and tet(M) were also frequently detected. Neither chlortetracycline nor tylosin increased the growth rate of pigs.

The residues and environmental risks of multiple veterinary antibiotics in animal faeces

To understand the residues and ecological risks of veterinary antibiotics (VAs) in animal faeces from concentrated animal feeding operations in northeastern China, 14 VAs were identified by high performance liquid chromatography, and the preliminary risks of six antibiotics were assessed using the hazard quotient (HQ). The investigated VAs occurred in 7.41 to 57.41 % of the 54 samples, and the levels ranged from 0.08 to 56.81 mg kg(-1). Tetracyclines were predominant with a maximum level of 56.81 mg kg(-1) mostly detected in pig faeces. Sulfonamides were common and detected with the highest concentration of 7.11 mg kg(-1). Fluoroquinolones were more widely detected in chicken faeces rather than in pig or cow faeces, which contained the dominant antibiotic enrofloxacin. In comparison, the residue of tylosin was less frequently found. The risk evaluations of the six antibiotics revealed that tetracyclines, especially oxytetracycline, displayed the greatest ecological risk because of its high HQ value of 15.75. The results of this study imply that multiple kinds of VAs were jointly used in animal feeding processes in the study area. These medicine residues in animal faeces may potentially bring ecological risks if the animal manure is not treated effectively.

Antimicrobial drug resistance in Escherichia coli from humans and food animals, United States, 1950-2002

Determining drug resistance trends will optimize treatment and public health responses.

We conducted a retrospective study of Escherichia coli isolates recovered from human and food animal samples during 1950–2002 to assess historical changes in antimicrobial drug resistance. A total of 1,729 E. coli isolates (983 from humans, 323 from cattle, 138 from chickens, and 285 from pigs) were tested for susceptibility to 15 antimicrobial drugs. A significant upward trend in resistance was observed for ampicillin (p<0.001), sulfonamide (p<0.001), and tetracycline (p<0.001). Animal strains showed increased resistance to 11/15 antimicrobial agents, including ampicillin (p<0.001), sulfonamide (p<0.01), and gentamicin (p<0.001). Multidrug resistance (≥3 antimicrobial drug classes) in E. coli increased from 7.2% during the 1950s to 63.6% during the 2000s. The most frequent co-resistant phenotype observed was to tetracycline and streptomycin (29.7%), followed by tetracycline and sulfonamide (29.0%). These data describe the evolution of resistance after introduction of new antimicrobial agents into clinical medicine and help explain the range of resistance in modern E. coli isolates.

Transfer of multidrug-resistant bacteria between intermingled ecological niches: the interface between humans, animals and the environment

The use of antimicrobial agents has been claimed to be the driving force for the emergence and spread of microbial resistance. However, several studies have reported the presence of multidrug-resistant bacteria in populations exposed to low levels of antimicrobial drugs or even never exposed. For many pathogens, especially those organisms for which asymptomatic colonization typically precedes infection (e.g., Enterococcus spp. and Escherichia coli), the selective effects of antimicrobial use can only be understood if we considerer all biological and environmental pathways which enable these bacteria, and the genes they carry, to spread between different biomes. This ecological framework provides an essential perspective for formulating antimicrobial use policies, precisely because it encompasses the root causes of these problems rather than merely their consequences.

The changing face of pathogen discovery and surveillance

The pace of pathogen discovery is rapidly accelerating. This reflects not only factors that enable the appearance and globalization of new microbial infections, but also improvements in methods for ascertaining the cause of a new disease. Innovative molecular diagnostic platforms, investments in pathogen surveillance (in wildlife, domestic animals and humans) and the advent of social media tools that mine the World Wide Web for clues indicating the occurrence of infectious-disease outbreaks are all proving to be invaluable for the early recognition of threats to public health. In addition, models of microbial pathogenesis are becoming more complex, providing insights into the mechanisms by which microorganisms can contribute to chronic illnesses like cancer, peptic ulcer disease and mental illness. Here, I review the factors that contribute to infectious-disease emergence, as well as strategies for addressing the challenges of pathogen surveillance and discovery.

Mutational and transcriptomic changes involved in the development of macrolide resistance in Campylobacter jejuni

Macrolide antibiotics are important for clinical treatment of infections caused by Campylobacter jejuni. Development of resistance to this class of antibiotics in Campylobacter is a complex process, and the dynamic molecular changes involved in this process remain poorly defined. Multiple lineages of macrolide-resistant mutants were selected by stepwise exposure of C. jejuni to escalating doses of erythromycin or tylosin. Mutations in target genes were determined by DNA sequencing, and the dynamic changes in the expression of antibiotic efflux transporters and the transcriptome of C. jejuni were examined by real-time reverse transcription-PCR, immunoblotting, and DNA microarray analysis. Multiple types of mutations in ribosomal proteins L4 and L22 occurred early during stepwise selection. On the contrary, the mutations in the 23S rRNA gene, mediating high resistance to macrolides, were observed only in the late-stage mutants. Upregulation of antibiotic efflux genes was observed in the intermediately resistant mutants, and the magnitude of upregulation declined with the occurrence of mutations in the 23S rRNA gene. DNA microarray analysis revealed the differential expression of 265 genes, most of which occurred in the intermediate mutant, including the upregulation of genes encoding ribosomal proteins and the downregulation of genes involved in energy metabolism and motility. These results indicate (i) that mutations in L4 and L22 along with temporal overexpression of antibiotic efflux genes precede and may facilitate the development of high-level macrolide resistance and (ii) that the development of macrolide resistance affects the pathways important for physiology and metabolism in C. jejuni, providing an explanation for the reduced fitness of macrolide-resistant Campylobacter.

Residues of veterinary medicinal products and coccidiostats in eggs – causes, control and results of surveillance program in Poland

The use of veterinary medicinal products in food producing animals for a variety of purposes causes that their residues may be presented in edible tissues. As a result, in concern of public health, European Union Countries establish each year monitoring plans and they control the levels of harmful substances in food of animal origin. This paper presents survey of residues of veterinary medicinal products and coccidiostats in eggs for Poland and European Union in years 2007-2010. Despite the decrease in reported non-compliant results for coccidiostats, the numbers were still higher than those for veterinary medicines. The most often determined coccidiostats were: nicarbazin, dinitrocarbanilide, salinomycin and lasalocid, and the most often reported non-compliant results for veterinary medicines were: antimicrobials, enrofloxacin and doxycycline.

Effects of the prebiotics inulin and lactulose on intestinal immunology and hematology of preruminant calves

Prebiotics are suggested as an alternative to antibiotics in animal rearing. Fermentable substances such as inulin or lactulose have been proposed to stimulate the immune system and health by modulation of the intestinal flora and its fermentation products. In this study, effects of inulin and lactulose on the intestinal health and hematology of calves have been investigated. Both prebiotics significantly decreased thrombocyte counts in peripheral blood. Only inulin was able to increase hemoglobin concentration and hematocrit. Total leukocyte count was decreased by lactulose while both prebiotics tended to lower monocyte proportions. mRNA expression of inflammation-related markers in the intestine was also affected by both prebiotics hinting at a decreased inflammatory status. This may be due to a possible decrease in intestinal pathogen load that remains to be verified. Only mRNA amounts of interleukin 8 were increased by lactulose in mesenteric lymph nodes. In the ileum, expression of a proliferation marker was increased by inulin while an apoptosis-related gene was increased by both prebiotics. The results of this study show a clear effect of prebiotics on certain parameters associated with animal health and performance that remain to be studied in detail in future investigations.

Phylogenetic analysis reveals common antimicrobial resistant Campylobacter coli population in antimicrobial-free (ABF) and commercial swine systems

The objective of this study was to compare the population biology of antimicrobial resistant (AR) Campylobacter coli isolated from swine reared in the conventional and antimicrobial-free (ABF) swine production systems at farm, slaughter and environment. A total of 200 C. coli isolates selected from fecal, environmental, and carcass samples of ABF (n = 100) and conventional (n = 100) swine production systems were typed by multilocus sequence typing (MLST). Sequence data from seven housekeeping genes was analyzed for the identification of allelic profiles, sequence types (STs) and clonal complex determination. Phylogenetic trees were generated to establish the relationships between the genotyped isolates. A total of 51 STs were detected including two novel alleles (glnA 424 and glyA 464) and 14 novel STs reported for the first time. The majority of the C. coli isolates belonged to ST-854 (ABF: 31, conventional: 17), and were grouped in clonal complex ST-828 (ABF: 68%, conventional: 66%). The mean genetic diversity (H) for the ABF (0.3963+/-0.0806) and conventional (0.4655+/-0.0714) systems were similar. The index of association (I(A)(S)) for the ABF (I(A)(S)= 0.1513) and conventional (I(A)(S) = 0.0991) C. coli populations were close to linkage equilibrium, indicative of a freely recombining population. Identical STs were detected between the pigs and their environment both at farm and slaughter. A minimum spanning tree revealed the close clustering of C. coli STs that originated from swine and carcass with those from the environment. In conclusion, our study reveals a genotypic diverse C. coli population that shares a common ancestry in the conventional and ABF swine production systems. This could potentially explain the high prevalence of antimicrobial resistant C. coli in the ABF system in the absence of antimicrobial selection pressure.

Vaccines and antibiotic resistance

Vaccines and antibiotics have significantly contributed to improve health and also to increase the longevity of human beings. The fast-acting effect of antibiotics makes them indispensable to treat infected patients. Likewise, when the causative agent of the infection is unknown and in cases of superinfections with different species of bacteria, antibiotics appear to be the only therapeutic option. On the contrary, vaccines are usually not efficacious in people already infected and their action is generally limited to a much narrowed range of pathogens. However, vaccines have contributed to the eradication of some of the most deadly infectious agents worldwide, can generate immunity to infections lasting for several years or life-long, and are able to induce herd immunity. Nonetheless, infectious diseases are still among the leading causes of morbidity and mortality worldwide. This is mainly owing to the emergence of bacterial resistance to antibiotics and the lack of efficacious medications to treat several other infectious diseases. Development of new vaccines appears to be a promising solution to these issues. Indeed, with the advent of new discovery approaches and adjuvants, today is possible to make vaccines virtually against every pathogen. In addition, while vaccine-resistant bacteria have never been reported, accumulating literature is providing evidence that vaccination can reduce the raise of antibiotic resistant strains by decreasing their use.

Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin

Antimicrobials have been used extensively as growth promoters (AGPs) in agricultural animal production. However, the specific mechanism of action for AGPs has not yet been determined. The work presented here was to determine and characterize the microbiome of pigs receiving one AGP, tylosin, compared with untreated pigs. We hypothesized that AGPs exerted their growth promoting effect by altering gut microbial population composition. We determined the fecal microbiome of pigs receiving tylosin compared with untreated pigs using pyrosequencing of 16S rRNA gene libraries. The data showed microbial population shifts representing both microbial succession and changes in response to the use of tylosin. Quantitative and qualitative analyses of sequences showed that tylosin caused microbial population shifts in both abundant and less abundant species. Our results established a baseline upon which mechanisms of AGPs in regulation of health and growth of animals can be investigated. Furthermore, the data will aid in the identification of alternative strategies to improve animal health and consequently production.

Prevalence and antimicrobial resistance of Cronobacter sakazakii isolated from domestic kitchens in middle Tennessee, United States

Cronobacter sakazakii is an emerging opportunistic pathogen that has been implicated in cases of severe meningitis, sepsis, and necrotizing enterocolitis in premature and full-term infants. In this study, the prevalence of C. sakazakii was estimated in selected domestic kitchens in middle Tennessee. Antimicrobial resistance patterns of these C. sakazakii isolates were examined for points of public health significance. A total of 234 contact sites in 78 domestic kitchens were tested for C. sakazakii. Consumers' used dishcloths and cleaning sponges were also tested. Antimicrobial susceptibility of the identified C. sakazakii isolates was determined for 10 antimicrobial drugs by means of the disk diffusion method. C. sakazakii was recovered from 26.9% of domestic kitchens visited. Multidrug resistance was observed; the highest resistance was to penicillin (76.1% of isolates) followed by tetracycline (66.6%), ciprofloxacin (57.1%), and nalidixic acid (47.6%). None of the C. sakazakii isolates were resistant to gentamicin. These results suggest that antibiotic-resistant C. sakazakii could be present at various sites in domestic kitchens.

A new Lactobacillus plantarum strain, TN8, from the gastro intestinal tract of poultry induces high cytokine production

This study aimed to determine the probiotic potential of 100 strains of Lactic Acid Bacteria (LAB) isolated from different intestinal segments of indigenous poultry in Tunisia. The strains were submitted to a battery of standard tests and criteria commonly used for determining their probiotic properties and attributes. The findings revealed that 19 of the isolates exhibited antimicrobial activity against 4 pathogenic bacteria, and that 4 (TN1, TN8, TN7, and TN13) showed good resistance to pH 3 and 5% bovine bile. Three isolates, namely TN1, TN8, and TN13, showed sensitivity to several antibiotics and were, therefore, selected for further enzymatic activity assays. Two isolates, namely TN1 and TN8, showed high efficacy of adhesion to chicken enterocytes. The cytokines released after stimulation by the two isolates showed high anti-inflammatory profiles, with an increased rate of Interleukin-10 (IL-10) production for the TN8 strain. Showing the highest performance, TN8 was submitted to 16S rRNA gene sequencing, which revealed that the strain was of the species Lactobacillus plantarum. Overall, the findings indicate that the Lactobacilli from poultry intestine has a number of promising properties that make it candidate for application as a probiotic additive in poultry industry.

Effect of streptomycin treatment on bacterial community structure in the apple phyllosphere

We studied the effect of many years of streptomycin use in apple orchards on the proportion of phyllosphere bacteria resistant to streptomycin and bacterial community structure. Leaf samples were collected during early July through early September from four orchards that had been sprayed with streptomycin during spring of most years for at least 10 years and four orchards that had not been sprayed. The percentage of cultured phyllosphere bacteria resistant to streptomycin at non-sprayed orchards (mean of 65%) was greater than at sprayed orchards (mean of 50%) (P = 0.0271). For each orchard, a 16S rRNA gene clone library was constructed from leaf samples. Proteobacteria dominated the bacterial communities at all orchards, accounting for 71 of 104 OTUs (determined at 97% sequence similarity) and 93% of all sequences. The genera Massilia, Methylobacterium, Pantoea, Pseudomonas, and Sphingomonas were shared across all sites. Shannon and Simpson's diversity indices and Pielou's evenness index were similar among orchards regardless of streptomycin use. Analysis of Similarity (ANOSIM) indicated that long-term streptomycin treatment did not account for the observed variability in community structure among orchards (R = -0.104, P = 0.655). Other variables, including time of summer, temperature and time at sampling, and relative distance of the orchards from each other, also had no significant effect on bacterial community structure. We conclude that factors other than streptomycin exposure drive both the proportion of streptomycin-resistant bacteria and phylogenetic makeup of bacterial communities in the apple phyllosphere in middle to late summer.