Molecular characterization of gentamicin-resistant Enterococci in the United States: evidence of spread from animals to humans through food

Effect of veterinary feed directive rule changes on tetracycline-resistant and erythromycin-resistant bacteria (Salmonella, Escherichia, and Campylobacter) in retail meats in the United States

BACKGROUND

Antimicrobial-resistant bacteria are a growing public health threat. In 2017 the U.S. Food and Drug Administration implemented Veterinary Feed Directive (VFD) rules changes to limit medically important antimicrobial use in food-producing animals, combating antimicrobial-resistant bacteria. The effect of the VFD rule changes on the occurrence of bacteria resistant to medically-important antimicrobials in retail meats is yet to be investigated in the U.S. This study investigates whether the VFD rule changes affected the occurrence of tetracycline-resistant and erythromycin-resistant bacteria (Salmonella, Escherichia, and Campylobacter) in retail meats in the U.S.

METHODS

Multivariable mixed effect logistic regression models were used to analyze 2002-2019 retail meats surveillance data from the National Antimicrobial Resistance Monitoring System (NARMS) in the U.S. Variables included VFD rule changes, meat type, quarter of year, and raising claims. A potential association between these variables and the occurrence of tetracycline-resistant and erythromycin-resistant bacteria (Salmonella, Escherichia, and Campylobacter) in retail meats was estimated.

RESULTS

Analysis included data regarding tetracycline-resistant Salmonella (n = 8,501), Escherichia (n = 20, 283), Campylobacter (n = 9,682), and erythromycin-resistant Campylobacter (n = 10,446) in retail meats. The odds of detecting tetracycline-resistant Escherichia (OR = 0.60), Campylobacter (OR = 0.89), and erythromycin-resistant Campylobacter (OR = 0.43) in chicken breast significantly decreased after the VFD rule changes, compared to the pre-VFD rule change period. The odds of detecting tetracycline-resistant Salmonella (0.66), Escherichia (OR = 0.56), and Campylobacter (OR = 0.33) in ground turkey also significantly decreased. However, the odds of detecting tetracycline-resistant Salmonella (OR = 1.49) in chicken breast and erythromycin-resistant Campylobacter (OR = 4.63) in ground turkey significantly increased. There was no significant change in the odds of detecting tetracycline-resistant Salmonella and Escherichia in ground beef or pork chops.

CONCLUSIONS

The implementation of VFD rule changes had a beneficial effect by reducing the occurrence of tetracycline-resistant and erythromycin-resistant bacteria in chicken and ground turkey. Ongoing surveillance of antimicrobial resistance and antimicrobial use could complement the implementation of stewardship such as VFD rule in food-producing animals in the U.S.

Antibiotic Resistance among Gastrointestinal Bacteria in Broilers: A Review Focused on Enterococcus spp. and Escherichia coli

Chickens can acquire bacteria at different stages, and bacterial diversity can occur due to production practices, diet, and environment. The changes in consumer trends have led to increased animal production, and chicken meat is one of the most consumed meats. To ensure high levels of production, antimicrobials have been used in livestock for therapeutic purposes, disease prevention, and growth promotion, contributing to the development of antimicrobial resistance across the resident microbiota. Enterococcus spp. and Escherichia coli are normal inhabitants of the gastrointestinal microbiota of chickens that can develop strains capable of causing a wide range of diseases, i.e., opportunistic pathogens. Enterococcus spp. isolated from broilers have shown resistance to at least seven classes of antibiotics, while E. coli have shown resistance to at least four. Furthermore, some clonal lineages, such as ST16, ST194, and ST195 in Enterococcus spp. and ST117 in E. coli, have been identified in humans and animals. These data suggest that consuming contaminated animal-source food, direct contact with animals, or environmental exposure can lead to the transmission of antimicrobial-resistant bacteria. Therefore, this review focused on Enterococcus spp. and E. coli from the broiler industry to better understand how antibiotic-resistant strains have emerged, which antibiotic-resistant genes are most common, what clonal lineages are shared between broilers and humans, and their impact through a One Health perspective.

The Pork Food Chain as a Route of Transmission of Antimicrobial Resistant Escherichia coli: A Farm-to-Fork Perspective

Antimicrobial resistance (AMR) is a public health risk that needs to be faced from a One Health perspective that includes humans, animals, and environmental health. The food production chain has been identified as a possible route of transmission of AMR bacteria to humans. The most critical phenomenon is related to Critically Important Antimicrobial (CIA) resistance. β-lactams antibiotics (cephalosporin of 3rd, 4th generation, carbapenem, monobactams, and penicillins), quinolones, aminoglycosides, polymyxin, and glycylcyclines were the CIAs chosen in this study. Samples derived from all the stages of the pork food production chain were collected, including pig feces, carcasses, and pork food products (fresh meat, fermented, and seasoned). Escherichia coli were isolated, and AMR and MDR profiles were evaluated. Enterobacterial Repetitive Intragenic Consensus (ERIC-PCR) was used to evaluate phylogenetic similarities. Data showed that 50% of phenotypical AMR observed in the entire pork food chain were related phylogenetically. The contamination of fresh meat, in half of the cases, was not directly related to contamination from feces or carcasses. Despite this, some similarities were found between feces and carcasses. In group analysis, phylogenetic similarities were detected in a 3/36 cluster (8.3%). Nevertheless, further studies are needed to improve consumer risk communication and access to clear and reliable information and health concerns on food labels.

Cholesterol-lowering effects and safety assessment of Lactobacillus spp. in vivo and in vitro testing for human use as probiotic from the dairy product in Egypt

BACKGROUND

The toxicity profile of lactobacilli may be strain dependent, so it should be considered for safe utilization of probiotics. Further, in vivo studies are necessary to evaluate their safety.

RESULT

The ability of various probiotic strains to hydrolyze bile salts has been confirmed without noticeable hemolytic activity. Results revealed the presence of α-glucosidase, β-glucosidase, α-galactosidase, and β-galactosidase activity in all investigated isolates, while none of the isolates produced the carcinogenic enzyme β-glucuronidase. The probiotic strains exhibited remarkable cholesterol-lowering impact. Also, we found no evidence of chronic toxicity under the experimental conditions based on gross pathological examination of the viscera and study of the spleen and liver weight ratios. These findings indicated that the investigated strains, either alone or combined with their metabolites, had no obvious adverse effect on the mice's general health status.

CONCLUSION

There is prove that the investigated probiotic strains are safe to be utilized for enhancing of the growth performance and are free of adverse side effects.

Prevalence and Characterization of Gentamicin Resistance Genes in Escherichia coli Isolates from Beef Cattle Feces in Japan

Gentamicin is an important antibiotic for the treatment of opportunistic infections in the clinical field. Gentamicin-resistant bacteria have been detected in livestock animals and can be transmitted to humans through the food supply or direct contact. We have previously revealed that gentamicin-resistant Escherichia coli are distributed at a comparatively high rate from beef cattle in Japan, but few studies have focused on the molecular epidemiology of gentamicin-resistant bacteria. To understand these bacteria, this study examined the prevalence of various gentamicin resistance genes in gentamicin-resistant E. coli isolates from beef cattle feces. Of the 239 gentamicin-resistant E. coli isolates, the presence of the aacC2, aadB, or aac(3)-VIa genes was confirmed in 147, 84, and 8 isolates, respectively. All aac(3)-VIa-harboring isolates had an MIC value of 64 μg/mL for gentamicin and exhibited resistance to 11 antibiotic agents. An analysis of the representative aac(3)-VIa-harboring E. coli strain GC1-3-GR-4 revealed that the aac(3)-VIa gene was present on the IncA/C plasmid together with the aadA and bla_CMY genes. Furthermore, the upstream region of the aac(3)-VIa gene contained the aadA gene and the class 1 integron-integrase gene (intI1). The aac(3)-VIa gene was detected for the first time in Japan and is expected to be able to transfer between bacteria via the IncA/C plasmid and integron. These results reveal the expansion of the distribution or diversity of gentamicin resistance genes in Japan.

Secondary plant metabolites as potent drug candidates against antimicrobial-resistant pathogens

Antibiotic resistance is a major public health threat of the twenty-first century and represents an important risk to the global economy. Healthcare-associated infections mainly caused by drug-resistant bacteria are wreaking havoc in patient care worldwide. The spread of such pathogens limits the utility of available drugs and complicates the treatment of bacterial diseases. As a result, there is an urgent need for new drugs with mechanisms of action capable of curbing resistance. Plants synthesize and utilize various metabolic compounds to deter pathogens and predators. Utilizing these plant-based metabolites is a promising option in identifying novel bioactive compounds that could be harnessed to develop new potent antimicrobial drugs to treat multidrug-resistant pathogens. The purpose of this review is to highlight medicinal plants as important sources of novel antimicrobial agents that could be developed to help combat antimicrobial resistance.

Risk Factors and Prevalence of mcr-1-Positive Escherichia coli in Fecal Carriages Among Community Children in Southern Taiwan

Colistin is the last resort antimicrobial for treating multidrug-resistant gram-negative bacterial infections. The plasmid-mediated colistin resistance gene, mcr-1, crucially influences colistin’s resistance transmission. Human fecal carriages of mcr-1-positive Escherichia coli (E. coli) were detected in many regions worldwide; however, only a few studies have focused on children. Therefore, we identified the prevalence and risk factors of mcr-1-positive E. coli in fecal carriages among community children in Southern Taiwan. In this study, 510 stool samples were collected from April 2016 to August 2019 from the pediatric department at a medical center in Southern Taiwan. These samples were collected within 3 days after admission and were all screened for the presence of the mcr-1 gene. Diet habits, travel history, pet contact, and medical history were also obtained from participants to analyze the risk factors of their fecal carriages to mcr-1-positive E. coli. Antimicrobial susceptibility testing was determined using the VITEK 2 system and the broth microdilution test. Twelve mcr-1-positive E. coli. were isolated from 2.4% of the fecal samples. Through multivariate analysis, frequent chicken consumption (at least 3 times per week) had a significantly positive association with the presence of mcr-1-positive E. coli in fecal carriages (adjust odds ratio 6.60, 95% confidence interval1.58– 27.62, p = 0.033). Additionally, multidrug resistance was more common in mcr-1-positive E. coli. (75.0% vs. 39.5%, p = 0.031) than in non-mcr-1-positive Escherichia coli. Furthermore, the percentage of extraintestinal pathogenic E. coli in mcr-1-positive isolates was 83.3%. Some multi-locus sequence types in our mcr-1-positive E. coli were also similar to those isolated from food animals in the literature. The prevalence of fecal carriages of mcr-1-positive E. coli was low among community children in Southern Taiwan. Our data shows that chicken consumption with a higher frequency increases the risk of mcr-1-positive E. coli. in fecal carriages.

Molecular characterization of antimicrobial resistance and virulence factors of Enterococcus faecalis from ducks at slaughterhouses

This study investigated the prevalence of antimicrobial resistant Enterococcus faecalis (E. faecalis) from ducks at slaughterhouses, analyzed antimicrobial resistance genes and virulence-associated genes of the isolates. Multilocus sequence typing (MLST) was performed to characterize their molecular characteristics. A total of 227 E. faecalis isolates (67.8%) were obtained from cecum (n = 114), cloaca (n = 50), skin (n = 59), and rinsed water (n = 4). These E. faecalis exhibited high level of resistance against tetracycline (95.6%), doxycycline (94.3%), linezolid (75.8%), erythromycin (72.2%), followed by norfloxacin (56.8%), vancomycin (38.3%), penicillin (36.1%), teicoplanin (30.8%). Lower level of resistance was found to high-level streptomycin (19.8%), imipenem (15.9%) and high-level gentamicin (5.7%). The vast majority of isolates (90.3%) were multidrug resistant (MDR). Moreover, the commonly observed resistance genes were optrA (90.7%) and ermB (90.3%), followed by aph(3’)-Ⅲ (86.8%), tetM (84.6%), acc(6’)-aph(2) (77.5%), blaZ (76.7%) and aac(6’)-Ie-aph(2”)-Ia (75.8%). The less frequently observed genes were vanC (19.8%), blaTEM (4.8%), vanM (2.6%), and vanA (0.4%). None of the strains carried aph(2”)-Ic and vanB genes. Furthermore, a high prevalence of ten virulence determinants was identified, and efaA (99.1%) was predominant, followed by eep (97.4%), srtA (96.9%), asa1 (95.6%), fsrB (92.1%), sprE (89.9%), aggA (63.9%), gelE (56.4%), esp (33.9%), and cylL (15.4%). Eleven isolates (4.9%) co-carried all of the tested virulence-associated genes. MLST analysis demonstrated that, E. faecalis isolates consisted of 12 known STs and 5 new STs, among which 6 of the identified STs were associated with nosocomial infection. Our data indicated that retail ducks serve as an important source of MDR E. faecalis with high pathogenicity potential, and suggested that transmission to humans could not be excluded.

Antimicrobial Resistance of Enterococcus sp. Isolated from Sheep and Goat Cheeses

This study aimed to calculate the proportion of antibiotic resistance profiles of Enterococcus faecium, E. faecalis, and E. durans isolated from traditional sheep and goat cheeses obtained from a selected border area of Slovakia with Hungary (region Slanské vrchy). A total of 110 Enterococcus sp. were isolated from cheese samples, of which 52 strains (E. faecium (12), E. faecalis (28), E. durans (12)) were represented. After isolation and identification by polymerase chain reaction and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry, the enterococci (E. faecium, E. faecalis, and E. durans) were submitted to susceptibility tests against nine antimicrobial agents. In general, strains of E. faecalis were more resistant than E. durans and E. faecium. A high percentage of resistance was noted in E. faecalis to rifampicin (100%), vancomycin (85.7%), teicoplanin (71.4%), erythromycin (71.4%), minocycline (57.1%), nitrofurantoin (57.1%), ciprofloxacin (14.3%), and levofloxacin (14.3%). E. durans showed resistance to rifampicin (100%), teicoplanin (100%), vancomycin (66.7%), erythromycin (66.7%), nitrofurantoin (66.7%), and minocycline (33.3%), and E. faecium showed resistance to vancomycin, teicoplanin, and erythromycin (100%). Multidrug-resistant strains were confirmed in 80% of the 52 strains in this study. Continuous identification of Enterococcus sp. and monitoring of their incidence and emerging antibiotic resistance is important in order to prevent a potential risk to public health caused by the contamination of milk and other dairy products, such as cheeses, made on farm level.

Gain and loss of antibiotic resistant genes in multidrug resistant bacteria: One Health perspective

The emergence of multidrug resistance (MDR) has become a global health threat due to the increasing unnecessary use of antibiotics. Multidrug resistant bacteria occur mainly by accumulating resistance genes on mobile genetic elements (MGEs), made possible by horizontal gene transfer (HGT). Humans and animal guts along with natural and engineered environments such as wastewater treatment plants and manured soils have proven to be the major reservoirs and hotspots of spreading antibiotic resistance genes (ARGs). As those environments support the dissemination of MGEs through the complex interactions that take place at the human-animal-environment interfaces, a growing One Health challenge is for multiple sectors to communicate and work together to prevent the emergence and spread of MDR bacteria. However, maintenance of ARGs in a bacterial chromosome and/or plasmids in the environments might place energy burdens on bacterial fitness in the absence of antibiotics, and those unnecessary ARGs could eventually be lost. This review highlights and summarizes the current investigations into the gain and loss of ARG genes in MDR bacteria among human-animal-environment interfaces. We also suggest alternative treatments such as combinatory therapies or sequential use of different classes of antibiotics/adjuvants, treatment with enzyme-inhibitors, and phage therapy with antibiotics to solve the MDR problem from the perspective of One Health issues.

Dietary supplementation with oregano essential oil and monensin in combination is antagonistic to growth performance of yearling Holstein bulls

Our previous work indicated that feeding oregano essential oil (OEO) in combination with monensin (MON) may not be mutually beneficial to dairy calf growth performance. To evaluate this observation further, a 240-d long-term growth experiment was conducted using 12 young growing Holstein bulls using a 2 × 2 factorial treatment arrangement. Main factors were OEO and MON arranged in 4 individual treatments: (1) ration fed without OEO or MON (control), (2) OEO fed at 26 mg/kg of dry matter (DM), (3) MON fed at 25 mg/kg of DM, and (4) OEO and MON fed in combination (OEO+MON). Holstein bulls were 70 d of age and similar in body weight (BW; 93.3 ± 4.54 kg) and individually fed for 240 d. The targeted feeding rates of OEO and MON were blended into 200 g of concentrate and top dressed each morning to a corn stalklage-based ration. Body weights, frame measurements, and blood samples were collected monthly. Interactions of OEO by MON were detected for BW, BW gain, average daily gain, and a trend for feed conversion. Bulls fed OEO or MON demonstrated greater final BW (368, 385, 381, and 358 kg for control, OEO, MON, and OEO+MON, respectively), and BW gains (278, 292, 285, and 265 kg) and average daily gain (1.16, 1.22, 1.19, 1.11 kg/d) were greatest for bulls fed OEO or MON compared with bulls fed OEO+MON; bulls fed the control were intermediate and similar to bulls fed MON. Intake of DM was greater for bulls fed OEO (6.55, 6.99, 6.60, and 6.42 kg/d) compared with bulls fed remaining treatments. Frame growth gain measurements for heart girth, abdominal girth, withers height, body length, and cannon bone circumference were similar for bulls fed all treatments. Serum triglyceride (0.23, 0.25, 0.28, and 0.24 mmol/L) concentrations were greater for bulls fed MON compared with bulls fed the control and OEO+MON, and bulls fed OEO were intermediate and similar. Cholesterol (2.06, 2.29, 2.20, and 2.07 mmol/L) concentrations were greater for bulls fed OEO compared with bulls fed the control and OEO+MON, and bulls fed MON were intermediate and similar. Serum antioxidant measurements were similar for bulls fed all treatments. Serum IgA, IgG, and IgM concentrations were similar for bulls fed all treatments. Feeding OEO or MON separately can improve growth performance of growing Holstein bulls. We do not know why the combination of OEO and MON is antagonistic to growth performance of Holstein bulls. However, these technologies should not be fed in combination to growing dairy cattle.

Food-to-Humans Bacterial Transmission

Microorganisms vehiculated by food might benefit health, cause minimal change within the equilibrium of the host microbial community or be associated with foodborne diseases. In this chapter we will focus on human pathogenic bacteria for which food is conclusively demonstrated as their transmission mode to human. We will describe the impact of foodborne diseases in public health, the reservoirs of foodborne pathogens (the environment, human and animals), the main bacterial pathogens and food vehicles causing human diseases, and the drivers for the transmission of foodborne diseases related to the food-chain, host or bacteria features. The implication of food-chain (foodborne pathogens and commensals) in the transmission of resistance to antibiotics relevant to the treatment of human infections is also evidenced. The multiplicity and interplay of drivers related to intensification, diversification and globalization of food production, consumer health status, preferences, lifestyles or behaviors, and bacteria adaptation to different challenges (stress tolerance and antimicrobial resistance) from farm to human, make the prevention of bacteria-food-human transmission a modern and continuous challenge. A global One Health approach is mandatory to better understand and minimize the transmission pathways of human pathogens, including multidrug-resistant pathogens and commensals, through food-chain.

A State-of-Art Review on Multi-Drug Resistant Pathogens in Foods of Animal Origin: Risk Factors and Mitigation Strategies

Most of the foodborne microbial diseases are linked to foods of animal origin such as milk, meat, and poultry. Nowadays, the presence of multi-drug resistant (MDR) pathogens in foods is becoming an increasingly public health concern worldwide due to the overuse of antimicrobial drugs in animal feed. MDR pathogens can enter the food chain by posing a significant risk to both animals and consumers. MDR pathogens causing infections are untreatable due to their resistance to various antibiotics, primarily cephalosporin and carbapenems and to their extended-spectrum beta-lactamase (ESBL)-producing capability. In addition, foods of animal origin and food-related environments can be likely vehicles for spreading of multi-drug resistance genes, which accelerates the thriving of global antibiotic resistance. This paper reviews the role of foods of animal origin as a vehicle for MDR pathogens, stressing the contribution of food processes, environments, and storage conditions in dissemination and reduction of antimicrobial resistances (AMRs). Controlling the growth of MDR microorganisms and limiting the transmission/expression of AMR genes in food ecosystems could be an effective mitigation strategy, putting the focus on food processes as a part of the solution for AMR in foods. Bioprotective cultures are also a promising and environmentally friendly technology to reduce the incidence of MDR pathogens, though caution is taken as microbial starters and probiotics can also carry AMR. Finally, applying Whole Genome Sequencing (WGS) and predictive microbiology, within a Risk Assessment framework, is key to get insight into those mechanisms and conditions along the food chain favoring or reducing AMR.

Data-Driven Analysis of Antimicrobial Resistance in Foodborne Pathogens from Six States within the US

Foodborne pathogens cause thousands of illnesses across the US each year. However, these pathogens gain resistance to the antimicrobials that are commonly used to treat them. Typically, antimicrobial resistance is caused by mechanisms encoded by multiple antimicrobial-resistance genes. These are carried through pathogens found in foods such as meats. It is, thus, important to study the genes that are most related to antimicrobial resistance, the pathogens, and the meats carrying antimicrobial-resistance genes. This information can be further used to correlate the antimicrobial-resistance genes found in humans for improving human health. Therefore, we perform the first multivariate statistical analysis of the antimicrobial-resistance gene data provided in the NCBI Pathogen Detection Isolates Browser database, covering six states that are geographically either in close proximity to one another (i.e., Pennsylvania (PA), Maryland (MD), and New York (NY)) or far (i.e., New Mexico (NM), Minnesota (MN), and California (CA)). Hundreds of multidimensional data points were projected onto a two-dimensional space that was specified by the first and second principal components, which were then categorized with a hierarchical clustering approach. It turns out that aadA, aph(3’’), aph(3’’)-Ib, aph(6)-I, aph(6)-Id, bla, blaCMY, tet, tet(A), and sul2 constructed the assembly of ten genes that were most commonly involved in antimicrobial resistance in these six states. While geographically close states like PA, MD and NY share more similar antimicrobial-resistance genes, geographically far states like NM, MN, and CA also contain most of these common antimicrobial-resistance genes. One potential reason for this spread of antimicrobial-resistance genes beyond the geographic limitation is that animal meats like chicken and turkey act as the carriers for the nationwide spread of these genes.

Independent Microevolution Mediated by Mobile Genetic Elements of Individual Clostridium difficile Isolates from Clade 4 Revealed by Whole-Genome Sequencing

Mobile genetic elements play a key role in the continuing evolution of Clostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4 C. difficile isolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/b with aac(6′) aph(2′′) instead of catD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.

Horizontal gene transfer of mobile genetic elements (MGEs) accounts for the mosaic genome of Clostridium difficile, leading to acquisition of new phenotypes, including drug resistance and reconstruction of the genomes. MGEs were analyzed according to the whole-genome sequences of 37 C. difficile isolates with a variety of sequence types (STs) within clade 4 from China. Great diversity was found in each transposon even within isolates with the same ST. Two novel transposons were identified in isolates ZR9 and ZR18, of which approximately one third to half of the genes showed heterogenous origins compared with the usual intestinal bacterial genes. Most importantly, catD, known to be harbored by Tn4453a/b, was replaced by aac(6′) aph(2′′) in isolates 2, 7, and 28. This phenomenon illustrated the frequent occurrence of gene exchanges between C. difficile and other enterobacteria with individual heterogeneity. Numerous prophages and CRISPR arrays were identified in C. difficile isolates of clade 4. Approximately 20% of spacers were located in prophage-carried CRISPR arrays, providing a new method for typing and tracing the origins of closely related isolates, as well as in-depth studies of the mechanism underlying genome remodeling. The rates of drug resistance were obviously higher than those reported previously around the world, although all isolates retained high sensitivity to vancomycin and metronidazole. The increasing number of C. difficile isolates resistant to all antibiotics tested here suggests the ease with which resistance is acquired in vivo. This study gives insights into the genetic mechanism of microevolution within clade 4.

IMPORTANCE Mobile genetic elements play a key role in the continuing evolution of Clostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4 C. difficile isolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/b with aac(6′) aph(2′′) instead of catD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.

Antimicrobial Resistance in Enterococcus spp. of animal origin

Enterococci are natural inhabitants of the intestinal tract in humans and many animals, including food-producing and companion animals. They can easily contaminate the food and the environment, entering the food chain. Moreover, Enterococcus is an important opportunistic pathogen, especially the species E. faecalis and E. faecium, causing a wide variety of infections. This microorganism not only contains intrinsic resistance mechanisms to several antimicrobial agents, but also has the capacity to acquire new mechanisms of antimicrobial resistance. In this review we analyze the diversity of enterococcal species and their distribution in the intestinal tract of animals. Moreover, resistance mechanisms for different classes of antimicrobials of clinical relevance are reviewed, as well as the epidemiology of multidrug-resistant enterococci of animal origin, with special attention given to beta-lactams, glycopeptides, and linezolid. The emergence of new antimicrobial resistance genes in enterococci of animal origin, such as optrA and cfr, is highlighted. The molecular epidemiology and the population structure of E. faecalis and E. faecium isolates in farm and companion animals is presented. Moreover, the types of plasmids that carry the antimicrobial resistance genes in enterococci of animal origin are reviewed.

Severity of drug resistance and co-existence of Enterococcus faecalis in diabetic foot ulcer infections

The genes encoding aminoglycoside resistance in Enterococcus faecalis may promote collateral aminoglycoside resistance in polymicrobial wounds. We studied a total of 100 diabetic foot ulcer samples for infection and found 60 samples to be polymicrobial, 5 to be monomicrobial, and 35 samples to be culture negative. A total of 65 E. faecalis isolates were screened for six genes coding for aminoglycoside resistance, antibiotic resistance patterns, and biofilm production. Infectious Diseases Society of America/International Working Group on the Diabetic Foot system was used to classify the wound ulcers. Majority of the subjects with culture-positive wound were recommended conservative management, while 14 subjects underwent amputation. Enterococcal isolates showed higher resistance for erythromycin, tetracycline, and ciprofloxacin. Isolates from grade 3 ulcer showed higher frequency of aac(6')-Ie-aph(2″)-Ia, while all the isolates were negative for aph(2″)-Ib, aph(2″)-Ic, and aph(2″)-Id. The isolates from grade 3 ulcers showed higher resistance to aminoglycosides as well as teicoplanin and chloramphenicol. All the 39 biofilm producers were obtained from polymicrobial wound and showed higher resistance when compared to biofilm non-producers. Higher frequency of isolates carrying aac(6')-Ie-aph(2″)-Ia in polymicrobial community showing resistance to key antibiotics suggests widespread distribution of aminoglycoside-resistant E. faecalis and their role in worsening diabetic foot ulcers.

Assessment of the Risk to Public Health due to Use of Antimicrobials in Pigs-An Example of Pleuromutilins in Denmark

Antibiotic consumption in pigs can be optimized by developing treatment guidelines, which encourage veterinarians to use effective drugs with low probability of developing resistance of importance for human health. In Denmark, treatment guidelines for use in swine production are currently under review at the Danish Veterinary and Food Administration. Use of pleuromutilins in swine has previously been associated with a very low risk for human health. However, recent international data and sporadic findings of novel resistance genes suggest a change of risk. Consequently, a reassessment was undertaken inspired by a risk assessment framework developed by the European Medicines Agency. Livestock-associated methicillin-resistant Staphylococcus aureus of clonal complex 398 (MRSA CC398) and enterococci were identified as relevant hazards. The release assessment showed that the probability of development of pleuromutilin resistance was high in MRSA CC398 (medium uncertainty) and low in enterococci (high uncertainty). A relatively small proportion of Danes has an occupational exposure to pigs, and foodborne transmission was only considered of relevance for enterococci, resulting in an altogether low exposure risk. The human consequences of infection with pleuromutilin-resistant MRSA CC398 or enterococci were assessed as low for the public in general but high for vulnerable groups such as hospitalized and immunocompromised persons. For MRSA CC398, the total risk was estimated as low (low uncertainty), among other due to the current guidelines on prevention of MRSA in place at Danish hospitals, which include screening of patients with daily contact to pigs on admittance. Moreover, MRSA CC398 has a medium human–human transmission potential. For enterococci, the total risk was estimated as low due to low prevalence of resistance, low probability of spread to humans, low virulence, but no screening of hospitalized patients, high ability of acquiring resistance genes, and a limited number of alternative antimicrobials (high uncertainty). This assessment reflects the current situation and should be repeated if pleuromutilin consumption increases substantially, resulting in increased prevalence of mobile, easily transmissible resistance mechanisms. Continuous monitoring of pleuromutilin resistance in selected human pathogens should therefore be considered. This also includes monitoring of linezolid resistance, since resistance mechanisms for pleuromutilins and oxazolidones are often coupled.

Interspecies transfer of vancomycin, erythromycin and tetracycline resistance among Enterococcus species recovered from agrarian sources

Background

Enterococci are now well recognised for their ability to transfer antibiotic resistance and for their association with nosocomial infections, but less is known regarding their relevance in the wider environment. Enterococcus faecalis and Enterococcus faecium were isolated from a range of agrarian associated sources (low-flow water, septic tank, poultry litter, high flow water, slurry/soil) and were assessed for latent ability to transfer antimicrobial resistance.

Results

The isolates were tested for phenotypic clumping in the presence of cell-free supernatant from other isolates. Some isolates were identified which demonstrated clumping, indicating that they possessed peptide sex pheromone conjugal machinery. All isolates were also tested for antibiotic resistance phenotypes using both disc diffusion and minimum inhibitory concentration (MIC) assays. These tests revealed that the enterococci demonstrated both phenotypic clumping and antibiotic resistance phenotypes. Based on these selection criteria, the isolates were identified as having the potential for horizontal gene transfer and were used to investigate the transfer of multiple antibiotic resistance phenotypes. Conjugal transfer of antibiotic resistance phenotypes was determined using a solid agar mating method followed by a standard antibiotic selection test resulting in different transfer patterns. An interspecies conjugal transfer of vancomycin resistance from E. faecalis to E. faecium was identified while the remaining reactions were within the same species. Transfer efficiencies ranging from 2 × 10⁻¹ to 2.3 × 10⁻⁵ were determined based on the reactions of three donor isolates (MF06036, MF0410 and MF06035) and two recipient isolates (MW01105^Rif and ST01109^Rif), with the transfer of vancomycin, erythromycin and tetracycline resistance genes.

Conclusions

The conjugation reactions and selection conditions used in this study resulted in a variety of co-transferred resistance phenotypes suggesting the presence of different mobile elements in the set of natural isolates. This study highlights the potential for extensive horizontal gene transfer in a previously neglected reservoir for enterococci.

[Probiotics as stimulators of immune response against pathogens in the respiratory tract]

This review analyzes whether.it is expedient to use oral probiotics for the stimulation of immune response against pathogens in the respiratory tract. It considers a relationship between.mucosal microbial colonization in different biotopes of the body and mucosal.immunity in the respiratory tract. The principal and terminological controversial issues of colonic dysbiosis and the possibilities of using the medicines and products containing live commensals/symbionts to correct microbiota disturbances are examined. There are data on the degree of resistance and resilience of the colonic microbial community exposed to destabilizing factors, antibiotics in particular. The properties of probiotics that have been proven to enhance host response against pathogens and the phenomena that characterize these probiotics as immunomodifiers and distinguish them from other immunostimulating/immunomodulating agents are described. Criteria for choosing effective and safe oral probiotics to stimulate an immune response in the respiratory tract are formulated. Finally, we review the data on the clinical and immunomodulatory effects of dietary supplement containing a combination of three probiotic strains (Lactobacillus gasseri PA 16/8, Bifidobacterium bifidum MF 20/5 and Bifidobacterium longum SP 07/3) with vitamins and minerals as an agent to prevent and reduce the severity of acute and recurrent respiratory tract infections.

Alternatives to overcoming bacterial resistances: State-of-the-art

Worldwide, bacterial resistance to chemical antibiotics has reached such a high level that endangers public health. Presently, the adoption of alternative strategies that promote the elimination of resistant microbial strains from the environment is of utmost importance. This review discusses and analyses several (potential) alternative strategies to current chemical antibiotics. Bacteriophage (or phage) therapy, although not new, makes use of strictly lytic phage particles as an alternative, or a complement, in the antimicrobial treatment of bacterial infections. It is being rediscovered as a safe method, because these biological entities devoid of any metabolic machinery do not possess any affinity whatsoever to eukaryotic cells. Lysin therapy is also recognized as an innovative antimicrobial therapeutic option, since the topical administration of preparations containing purified recombinant lysins with amounts in the order of nanograms, in infections caused by Gram-positive bacteria, demonstrated a high therapeutic potential by causing immediate lysis of the target bacterial cells. Additionally, this therapy exhibits the potential to act synergistically when combined with certain chemical antibiotics already available on the market. Another potential alternative antimicrobial therapy is based on the use of antimicrobial peptides (AMPs), amphiphilic polypeptides that cause disruption of the bacterial membrane and can be used in the treatment of bacterial, fungal and viral infections, in the prevention of biofilm formation, and as antitumoral agents. Interestingly, bacteriocins are a common strategy of bacterial defense against other bacterial agents, eliminating the potential opponents of the former and increasing the number of available nutrients in the environment for their own growth. They can be applied in the food industry as biopreservatives and as probiotics, and also in fighting multi-resistant bacterial strains. The use of antibacterial antibodies promises to be extremely safe and effective. Additionally, vaccination emerges as one of the most promising preventive strategies. All these will be tackled in detail in this review paper.

Probiotic approach to prevent antibiotic resistance

Probiotics are live microorganisms, mainly belonging to the genera Lactobacillus and Bifidobacterium, although also strain of other species are commercialized, that have a beneficial effect on the host. From the perspective of antibiotic use, probiotics have been observed to reduce the risk of certain infectious disease such as certain types of diarrhea and respiratory tract infection. This may be accompanied with a reduced need of antibiotics for secondary infections. Antibiotics tend to be effective against most common diseases, but increasingly resistance is being observed among pathogens. Probiotics are specifically selected to not contribute to the spread of antibiotic resistance and not carry transferable antibiotic resistance. Concomitant use of probiotics with antibiotics has been observed to reduce the incidence, duration and/or severity of antibiotic-associated diarrhea. This contributes to better adherence to the antibiotic prescription and thereby reduces the evolution of resistance. To what extent probiotics directly reduce the spread of antibiotic resistance is still much under investigation; but maintaining a balanced microbiota during antibiotic use may certainly provide opportunities for reducing the spread of resistances. Key messages Probiotics may reduce the risk for certain infectious diseases and thereby reduce the need for antibiotics. Probiotics may reduce the risk for antibiotic-associated diarrhea Probiotics do not contribute to the spread of antibiotic resistance and may even reduce it.

Multiple antibiotic resistances among Shiga toxin producing Escherichia coli O157 in feces of dairy cattle farms in Eastern Cape of South Africa

Background

Shiga toxin–producing Escherichia coli (STEC) O157:H7 is a well-recognized cause of bloody diarrhea and hemolytic-uremic syndrome (HUS). The ability of STEC strains to cause human disease is due to the production of Shiga toxins. The objectives of this study were to determinate the prevalence, serotypes, antibiotic susceptibility patterns and the genetic capability for Shiga toxin production in Escherichia coli (STEC) strains isolated from dairy cattle farms in two rural communities in the Eastern Cape Province of South Africa.

Methods

Fecal samples were collected between March and May 2014, from individual cattle (n = 400) in two commercial dairy farms having 800 and 120 cattle each.

Three hundred presumptive isolates obtained were subjected to polymerase chain reactions (PCR) for identification of O157 serogroup and Shiga toxin producing genes (stx1, stx2) on genomic DNA extracted by boiling method. Susceptibility of the isolates to 17 antibiotics was carried out in vitro by the standardized agar disc-diffusion method.

Results

Based on direct PCR detection, 95 (31.7 %) isolates were identified as O157 serogroup. The genetic repertoire for Shiga toxin production was present in 84 (88.42 %) isolates distributed as stx1 (37), stx2 (38) and stx1/2 (9) respectively while 11 of the isolates did not harbor Shiga toxin producing genes. Multiple antibiotic resistances were observed among the isolates and genetic profiling of resistance genes identified bla_ampC 90 %, bla_CMY 70 %, bla_CTX-M 65 %, bla_TEM 27 % and tetA 70 % and strA 80 % genes among the antimicrobial resistance determinants examined.

Conclusion

We conclude that dairy cattle farms in the Eastern Cape Province are potential reservoirs of antibiotic resistance determinants in the province.

Novel gentamicin resistance genes in Campylobacter isolated from humans and retail meats in the USA

OBJECTIVES

To understand the molecular epidemiology of gentamicin-resistant Campylobacter and investigate aminoglycoside resistance mechanisms.

METHODS

One-hundred-and-fifty-one gentamicin-resistant Campylobacter isolates from humans (n = 38 Campylobacter jejuni; n = 41, Campylobacter coli) and retail chickens (n = 72 C. coli), were screened for the presence of gentamicin resistance genes by PCR and subtyped using PFGE. A subset of the isolates (n = 41) was analysed using WGS.

RESULTS

Nine variants of gentamicin resistance genes were identified: aph(2″)-Ib, Ic, Ig, If, If1, If3, Ih, aac(6')-Ie/aph(2″)-Ia and aac(6')-Ie/aph(2″)-If2. The aph(2″)-Ib, Ic, If1, If3, Ih and aac(6')-Ie/aph(2″)-If2 variants were identified for the first time in Campylobacter. Human isolates showed more diverse aminoglycoside resistance genes than did retail chicken isolates, in which only aph(2″)-Ic and -Ig were identified. The aph(2″)-Ig gene was only gene shared by C. coli isolates from human (n = 27) and retail chicken (n = 69). These isolates displayed the same resistance profile and similar PFGE patterns, suggesting that contaminated retail chicken was probably the source of human C. coli infections. Human isolates were genetically diverse and generally more resistant than the retail chicken isolates. The most frequent co-resistance was to tetracycline (78/79, 98.7%), followed by ciprofloxacin/nalidixic acid (46/79, 58.2%), erythromycin and azithromycin (36/79, 45.6%), telithromycin (32/79, 40.5%) and clindamycin (18/79, 22.8%). All human and retail meat isolates were susceptible to florfenicol.

CONCLUSIONS

This study demonstrated that several new aminoglycoside resistance genes underlie the recent emergence of gentamicin-resistant Campylobacter, and that, in addition to contaminated retail chicken, other sources have also contributed to gentamicin-resistant Campylobacter infections in humans.

Occurrence and antimicrobial resistance of enterococci isolated from organic and conventional retail chicken

Antibiotic-resistant bacteria existing in agricultural environments may be transferred to humans through food consumption or more multifaceted environmental paths of exposure. Notably, enterococcal infections are becoming more challenging to treat as their resistance to antibiotics intensifies. In this study, the prevalence and antibiotic resistance profiles of enterococci in organic and conventional chicken from retail stores were analyzed. Of the total 343 retail chicken samples evaluated, 282 (82.2%) were contaminated with Enterococcus spp. The prevalence was higher in organic chicken (62.5%) than conventional chicken (37.5%). Enterococcus isolates were submitted to susceptibility tests against 12 antimicrobial agents. Among the isolates tested, streptomycin had the highest frequencies of resistance (69.1 and 100%) followed by erythromycin (38.5 and 80.0%), penicillin (14.1 and 88.5%), and kanamycin (11.3 and 76.9%) for organic and conventional isolates, respectively. Chloramphenicol had the lowest frequency (0.0 and 6.6%, respectively). The predominant species in raw chicken was E. faecium (27.3%), followed by E. gallinarum (6.0%), E. casseliflavus (2.1%), and E. durans (1.4%). These species were also found to be resistant to three or more antibiotics. The data indicated that antibiotic-resistant enterococci isolates were found in chicken whether it was organic or conventional. However, enterococci isolates that were resistant to antibiotics were less common in organic chicken (31.0%) when compared with those isolated from conventional chicken (43.6%). The results of this study suggest that raw retail organic and conventional chickens could be a source of antibiotic-resistant enterococci.

Food System Policy, Public Health, and Human Rights in the United States

The US food system functions within a complex nexus of social, political, economic, cultural, and ecological factors. Among them are many dynamic pressures such as population growth, urbanization, socioeconomic inequities, climate disruption, and the increasing demand for resource-intensive foods that place immense strains on public health and the environment. This review focuses on the role that policy plays in defining the food system, particularly with regard to agriculture. It further examines the challenges of making the food supply safe, nutritious, and sustainable, while respecting the rights of all people to have access to adequate food and to attain the highest standard of health. We conclude that the present US food system is largely unhealthy, inequitable, environmentally damaging, and insufficiently resilient to endure the impacts of climate change, resource depletion, and population increases, and is therefore unsustainable. Thus, it is imperative that the US embraces policy reforms to transform the food system into one that supports public health and reflects the principles of human rights and agroecology for the benefit of current and future generations.

Transmission dynamics of resistant bacteria in a predator-prey system

This paper discusses the impact on human health caused by the addition of antibiotics in the feed of food animals. We use the established transmission rule of resistant bacteria and combine it with a predator-prey system to determine a differential equations model. The equations have three steady equilibrium points corresponding to three population dynamics states under the influence of resistant bacteria. In order to quantitatively analyze the stability of the equilibrium points, we focused on the basic reproduction numbers. Then, both the local and global stability of the equilibrium points were quantitatively analyzed by using essential mathematical methods. Numerical results are provided to relate our model properties to some interesting biological cases. Finally, we discuss the effect of the two main parameters of the model, the proportion of antibiotics added to feed and the predation rate, and estimate the human health impacts related to the amount of feed antibiotics used. We further propose an approach for the prevention of the large-scale spread of resistant bacteria and illustrate the necessity of controlling the amount of in-feed antibiotics used.

Insects represent a link between food animal farms and the urban environment for antibiotic resistance traits

Antibiotic-resistant bacterial infections result in higher patient mortality rates, prolonged hospitalizations, and increased health care costs. Extensive use of antibiotics as growth promoters in the animal industry represents great pressure for evolution and selection of antibiotic-resistant bacteria on farms. Despite growing evidence showing that antibiotic use and bacterial resistance in food animals correlate with resistance in human pathogens, the proof for direct transmission of antibiotic resistance is difficult to provide. In this review, we make a case that insects commonly associated with food animals likely represent a direct and important link between animal farms and urban communities for antibiotic resistance traits. Houseflies and cockroaches have been shown to carry multidrug-resistant clonal lineages of bacteria identical to those found in animal manure. Furthermore, several studies have demonstrated proliferation of bacteria and horizontal transfer of resistance genes in the insect digestive tract as well as transmission of resistant bacteria by insects to new substrates. We propose that insect management should be an integral part of pre- and postharvest food safety strategies to minimize spread of zoonotic pathogens and antibiotic resistance traits from animal farms. Furthermore, the insect link between the agricultural and urban environment presents an additional argument for adopting prudent use of antibiotics in the food animal industry.

Virulence, antibiotic resistance and biogenic amines of bacteriocinogenic lactococci and enterococci isolated from goat milk

The present study aimed to investigate the virulence, antibiotic resistance and biogenic amine production in bacteriocinogenic lactococci and enterococci isolated from goat milk in order to evaluate their safety. Twenty-nine bacteriocinogenic lactic acid bacteria (LAB: 11 Lactococcus spp., and 18 Enterococcus spp.) isolated from raw goat milk were selected and subjected to PCR to identify gelE, cylA, hyl, asa1, esp, efaA, ace, vanA, vanB, hdc1, hdc2, tdc and odc genes. The expression of virulence factors (gelatinase, hemolysis, lipase, DNAse, tyramine, histamine, putrescine) in different incubation temperatures was assessed by phenotypic methods, as well as the resistance to vancomycin, gentamicin, chloramphenicol, ampicillin and rifampicin (using Etest®). The tested isolates presented distinct combinations of virulence related genes, but not necessarily the expression of such factors. The relevance of identifying virulence-related genes in bacteriocinogenic LAB was highlighted, demanding for care in their usage as starter cultures or biopreservatives due to the possibility of horizontal gene transfer to other bacteria in food systems.

Prevalence and phenotypic characterization of Enterococcus spp. isolated from food in Brazil

We evaluated the frequency of enterococci from food and found 95.2% of positivity, being E. faecium and E. faecalis the most frequent species. High-level streptomycin resistance was observed, as well as gelatinase and hemolysis activity, showing the potential role of environmental strains as reservoir of virulence and resistance traits.

High level aminoglycoside resistance and distribution of aminoglycoside resistant genes among clinical isolates of Enterococcus species in Chennai, India

Enterococci are nosocomial pathogen with multiple-drug resistance by intrinsic and extrinsic mechanisms. Aminoglycosides along with cell wall inhibitors are given clinically for treating enterococcal infections. 178 enterococcal isolates were analyzed in this study. E. faecalis is identified to be the predominant Enterococcus species, along with E. faecium, E. avium, E. hirae, E. durans, E. dispar and E. gallinarum. High level aminoglycoside resistance (HLAR) by MIC for gentamicin (GM), streptomycin (SM) and both (GM + SM) antibiotics was found to be 42.7%, 29.8%, and 21.9%, respectively. Detection of aminoglycoside modifying enzyme encoding genes (AME) in enterococci was identified by multiplex PCR for aac(6')-Ie-aph(2'')-Ia; aph(2'')-Ib; aph(2'')-Ic; aph(2'')-Id and aph(3')-IIIa genes. 38.2% isolates carried aac(6')-Ie-aph(2'')-Ia gene and 40.4% isolates carried aph(3')-IIIa gene. aph(2'')-Ib; aph(2'')-Ic; aph(2'')-Id were not detected among our study isolates. aac(6')-Ie-aph(2'')-Ia and aph(3')-IIIa genes were also observed in HLAR E. durans, E. avium, E. hirae, and E. gallinarum isolates. This indicates that high level aminoglycoside resistance genes are widely disseminated among isolates of enterococci from Chennai.

Genetic characterization of antibiotic resistance and virulence factors in Enterococcus spp. from Japanese retail ready-to-eat raw fish

Little information is available on the diversity and distribution of resistance and virulence factors in enterococci isolated from retail fish. In this study, 200 samples of retail ready-to-eat raw fish (sashimi) collected from the Japanese prefecture of Hiroshima were analyzed for incidence of Enterococcus spp. We recovered 96 enterococcal isolates from 90 (45%, 90/200) samples. Fifty-six strains were identified at the species level: E. faecalis (n = 31), E. faecium (n = 7), E. casseliflavus (n = 7), E. gallinarum (n = 3), E. phoeniculicola (n = 4), E. raffinosus (n = 2), E. saccharolyticus (n = 1), and E. gilvus (n = 1). Twenty-five (26%, 25/96) strains carried antibiotic resistance genes. These included the tet(M), tet(L), tet(K), erm(B), msr(A/B), aph(3'), and blaZ genes, which were detected in 12.5%, 9.3%, 2%, 14.5%, 1%, 1%, and 2% of isolates, respectively. The virulence genes gelE and asa1 were detected in 31 and 24 E. faecalis strains, respectively. Both genes were detected in one E. faecium strain. In conclusion, this is the first study to underscore the importance of sashimi as not only a reservoir of Enterococcus spp. carrying resistance and virulence genes, but also a reservoir for unusual Enterococcus spp.

A systematic quantitative proteomic examination of multidrug resistance in Acinetobacter baumannii

Multidrug-resistant Acinetobacter baumannii strains have been examined at the DNA sequence level, but seldom using large-scale quantitative proteomics. We have compared the proteome of the multidrug resistant strain BAA-1605, with the proteome of the drug-sensitive strain ATCC 17978, using iTRAQ labeling and online 2D LC/MS/MS for peptide/protein identification. Of 1484 proteins present in at least 2 of 4 independent experiments, 114 are 2-fold to 66-fold more abundant in BAA-1605, and 99 are 2-fold to 50-fold less abundant. Proteins with 2-fold or greater abundance in the multidrug resistant strain include drug-, antibiotic-, and heavy metal-resistance proteins, stress-related proteins, porins, membrane transporters, proteins important for acquisition of foreign DNA, biofilm-related proteins, cell-wall and exopolysaccharide-related proteins, lipoproteins, metabolic proteins, and many with no annotated function. The porin CarO, inactivated in carbapenem-resistant strains, is 2.3-fold more abundant in BAA-1605. Likewise, the porin OmpW, less abundant in carbapenem- and colistin-resistant A. baumannii strains, is 3-fold more abundant in BAA-1605. Nine proteins, all present in the drug-sensitive strain but from 2.2-fold to 16-fold more abundant in the MDR strain, can potentially account for the observed resistance of BAA-1605 to 18 antibiotics.

BIOLOGICAL SIGNIFICANCE

Multidrug resistant (MDR) strains of the pathogen Acinetobacter baumannii are a significant cause of hospital-acquired infections, are associated with increased mortality and length of stay, and may be a major factor underlying the spread of this pathogen, which is difficult to eradicate from clinical settings. To obtain a better understanding of antimicrobial resistance mechanisms in MDR A. baumannii, we report the first large scale 2D LC/MS/MS-based quantitative proteomics comparison of a drug-sensitive strain and an MDR strain of this pathogen. Ca. 20% of the expressed proteome changes 2-fold or more between the compared strains, including 42 proteins with literature or informatics annotations related to resistance mechanisms, modification of xenobiotics, or drug transport. Other categories of proteins differing 2-fold or more between strains include stress-response related proteins, porins, OMPs, transporters and secretion-related proteins, cell wall- and expolysaccharide-related proteins, lipoproteins, and DNA- and plasmid-related proteins. While the compared strains also differ in other aspects than multi-drug resistance, the observed differences, combined with protein functional annotation, suggest that complex protein expression changes may accompany the MDR phenotype. Expression changes of nine proteins in the MDR strain can potentially account for the observed resistance to 18 antibiotics.

Molecular characterization of high-level gentamicin-resistant Enterococcus faecalis from chicken meat in Korea

Because the intrinsically antimicrobial-resistant Enterococcus has acquired high-level aminoglycoside resistance genes, treating enterococcal infections is difficult. In this study, of the 101 food-borne Enterococcus faecalis isolates collected from retail chicken meat between 2003 and 2010, 11 high-level gentamicin-resistant (HLGR) E. faecalis isolates (MICs>2,048 μg/mL) were found. Molecular characterization was performed to determine the basis of this resistance. All HLGR E. faecalis isolates encoded aac(6')-Ie-aph(2″)-Ia and harbored at least 3 virulence traits in the asa1, esp, gelE, efaA, ace, and cylA genes. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were performed to characterize their molecular epidemiology. A total of 8 sequence types (STs), including 3 novel STs, were identified (ST35, ST82, ST116, ST202, ST300, ST403, ST407, and ST420). ST82, which is associated with amyloid arthropathy in poultry, was the most prevalent ST among HLGR E. faecalis isolates (4 out of 11 isolates, 36.4%); all other STs were identified in the isolates as well. The STs of food-borne HLGR E. faecalis in this study have been confirmed as corresponding to clinical isolates in the MLST database (DB), except for ST300 and the new STs. Three out of 11 isolates belonged to CC116, including ST116, ST407, and ST420. This study characterized HLGR E. faecalis isolates and provided evidence for the spread of HLGR E. faecalis with virulence factors to chicken sources in Korea. The emergence of food-borne HLGR E. faecalis suggests that chicken could be a potential source of transmission of antimicrobial resistance and virulence factors.

Antimicrobial resistance of Enterococcus species from meat and fermented meat products isolated by a PCR-based rapid screening method

Enterococci are predominantly found in the gastrointestinal tract of humans and animals, but species commonly resident on vegetation are known. Their presence in large numbers in foods may indicate a lapse in sanitation and their ability to serve as a genetic reservoir of transferable antibiotic resistance is of concern. Conventional culture methods for identification of enterococci are slow and sometimes give false results because of the biochemical diversity of the organisms in this genus. This work reports the development of a PCR-based assay to detect enterococci at the genus level by targeting a 16S rRNA sequence. Published 16S rRNA sequences were aligned and used to design genus specific primers (EntF and EntR). The primers were able to amplify a 678 bp target region from Enterococcus faecalis ATCC 7080 and 20 other strains of enterococci from 11 different species, but there was no amplification by 32 species from closely related genera (Pediococcus, Lactobacillus, Streptococcus and Listeria) or species of Escherichia coli and Salmonella. The PCR positive samples were plated, screened by a colony patch technique and their identities were confirmed by API 20 Strep panels and sequencing. When dry fermented sausage and ham as well as fresh meat batter for dry cured sausage manufacture were tested for enterococci by the method, 29 Enterococcus strains (15 E. faecalis, 13 E. faecium, and one E. gallinarum) were identified. When susceptibility of these enterococci to 12 antibiotics was tested, the highest incidence of resistance was to clindamycin (89.6%), followed by tetracycline hydrochloride (65.5%), tylosin (62%), erythromycin (45%), streptomycin and neomycin (17%), chloramphenicol (10.3%), penicillin (10.3%), ciprofloxacin (10.3%) and gentamicin (3.4%). None was resistant to the clinically important drugs vancomycin or ampicillin. Most strains (27/29) were resistant to more than one antibiotic while 17 of 29 strains were resistant to three to 8 antibiotics. The molecular method developed was validated for speciation of enterococci and was useful in assessing uncooked processed meat products as a reservoir for multi-drug resistant Enterococcus species.

Antimicrobial activity, antibiotic susceptibility and virulence factors of Lactic Acid Bacteria of aquatic origin intended for use as probiotics in aquaculture

Background

The microorganisms intended for use as probiotics in aquaculture should exert antimicrobial activity and be regarded as safe not only for the aquatic hosts but also for their surrounding environments and humans. The objective of this work was to investigate the antimicrobial/bacteriocin activity against fish pathogens, the antibiotic susceptibility, and the prevalence of virulence factors and detrimental enzymatic activities in 99 Lactic Acid Bacteria (LAB) (59 enterococci and 40 non-enterococci) isolated from aquatic animals regarded as human food.

Results

These LAB displayed a broad antimicrobial/bacteriocin activity against the main Gram-positive and Gram-negative fish pathogens. However, particular safety concerns based on antibiotic resistance and virulence factors were identified in the genus Enterococcus (86%) (Enterococcus faecalis, 100%; E. faecium, 79%). Antibiotic resistance was also found in the genera Weissella (60%), Pediococcus (44%), Lactobacillus (33%), but not in leuconostocs and lactococci. Antibiotic resistance genes were found in 7.5% of the non-enterococci, including the genera Pediococcus (12.5%) and Weissella (6.7%). One strain of both Pediococcus pentosaceus and Weissella cibaria carried the erythromycin resistance gene mef(A/E), and another two P. pentosaceus strains harboured lnu(A) conferring resistance to lincosamides. Gelatinase activity was found in E. faecalis and E. faecium (71 and 11%, respectively), while a low number of E. faecalis (5%) and none E. faecium exerted hemolytic activity. None enterococci and non-enterococci showed bile deconjugation and mucin degradation abilities, or other detrimental enzymatic activities.

Conclusions

To our knowledge, this is the first description of mef(A/E) in the genera Pediococcus and Weissella, and lnu(A) in the genus Pediococcus. The in vitro subtractive screening presented in this work constitutes a valuable strategy for the large-scale preliminary selection of putatively safe LAB intended for use as probiotics in aquaculture.

Antibiotic-resistant Enterococcus faecalis in abattoir pigs and plasmid colocalization and cotransfer of tet(M) and erm(B) genes

This study was conducted to determine plasmid colocalization and transferability of both erm(B) and tet(M) genes in Enterococcus faecalis isolates from abattoir pigs in Canada. A total of 124 E. faecalis isolates from cecal contents of abattoir pigs were examined for antibiotic susceptibility. High percentages of resistance to macrolides and tetracyclines were found. Two predominant multiresistance patterns of E. faecalis were examined by PCR and sequencing for the presence of genes encoding antibiotic resistance. Various combinations of antibiotic resistance genes were detected; erm(B) and tet(M) were the most common genes. Plasmid profiling and hybridization revealed that both genes were colocated on a ~9-kb transferable plasmid in six strains with the two predominant multiresistant patterns. Plasmid colocalization and cotransfer of tet(M) and erm(B) genes in porcine E. faecalis isolates indicates that antibiotic coselection and transferability could occur via this single genetic element. To our knowledge, this is the first report on plasmid colocalization and transferability of erm(B) and tet(M) genes in E. faecalis on a mobile genetic element of ~9 kb. Physical linkage between important antibiotic resistance determinants in enterococci is of interest for predicting potential transfer to other bacterial genera.

Enterococcus faecalis clones in poultry and in humans with urinary tract infections, Vietnam

Transmission routes and reservoirs need to be elucidated.

Enterococcus spp. as pathogens have increased, but the sources of infection often remain unclear. To investigate whether poultry might be a reservoir for E. faecalis–associated urinary tract infections (UTIs) in humans, we characterized E. faecalis isolates from patients in Vietnam with UTIs during January 2008–January 2010 and poultry living in close contact with them by multilocus sequence typing (MLST), pulsed-field gel electrophoresis, analysis of antimicrobial drug susceptibility patterns, and sequencing of virulence genes. In 7 (23%) of 31 UTI cases, we detected identical MLST, indistinguishable or closely related pulsed-field gel electrophoresis patterns, and similar antimicrobial drug susceptibility patterns. Isolates from urine and poultry showed identical virulence gene profiles, except for 1 variation, and individual genes showed identical sequences. The homology of isolates from urine and poultry further indicates the zoonotic potential and global spread of E. faecalis sequence type 16, which recently was reported in humans with endocarditis and in pigs in Denmark.