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254601.0000Clinical considerations on antimicrobial resistance potential of complex microbiological samples. Antimicrobial resistance (AMR) is one of our greatest public health challenges. Targeted use of antibiotics (ABs) can reduce the occurrence and spread of AMR and boost the effectiveness of treatment. This requires knowledge of the AB susceptibility of the pathogens involved in the disease. Therapeutic recommendations based on classical AB susceptibility testing (AST) are based on the analysis of only a fraction of the bacteria present in the disease process. Next and third generation sequencing technologies allow the identification of antimicrobial resistance genes (ARGs) present in a bacterial community. Using this metagenomic approach, we can map the antimicrobial resistance potential (AMRP) of a complex, multi-bacterial microbial sample. To understand the interpretiveness of AMRP, the concordance between phenotypic AMR properties and ARGs was investigated by analyzing data from 574 Escherichia coli strains of five different studies. The overall results show that for 44% of the studied ABs, phenotypically resistant strains are genotypically associated with a 90% probability of resistance, while for 92% of the ABs, the phenotypically susceptible strains are genotypically susceptible with a 90% probability. ARG detection showed a phenotypic prediction with at least 90% confidence in 67% of ABs. The probability of detecting a phenotypically susceptible strain as resistant based on genotype is below 5% for 92% of ABs. While the probability of detecting a phenotypically resistant strain as susceptible based on genotype is below 5% for 44% of ABs. We can assume that these strain-by-strain concordance results are also true for bacteria in complex microbial samples, and conclude that AMRP obtained from metagenomic ARG analysis can help choose efficient ABs. This is illustrated using AMRP by a canine external otitis sample.202539897495
510610.9997Metagenomic diagnostics for the simultaneous detection of multiple pathogens in human stool specimens from Côte d'Ivoire: a proof-of-concept study. BACKGROUND: The intestinal microbiome is a complex community and its role in influencing human health is poorly understood. While conventional microbiology commonly attributes digestive disorders to a single microorganism, a metagenomic approach can detect multiple pathogens simultaneously and might elucidate the role of microbial communities in the pathogenesis of intestinal diseases. We present a proof-of-concept that a shotgun metagenomic approach provides useful information on the diverse composition of intestinal pathogens and antimicrobial resistance profiles in human stool samples. METHODS: In October 2012, we obtained stool specimens from patients with persistent diarrhea in south Côte d'Ivoire. Four stool samples were purposefully selected and subjected to microscopy, multiplex polymerase chain reaction (PCR), and a metagenomic approach. For the latter, we employed the National Center for Biotechnology Information nucleotide database and screened for 36 pathogenic organisms (bacteria, helminths, intestinal protozoa, and viruses) that may cause digestive disorders. We further characterized the bacterial population and the prevailing resistance patterns by comparing our metagenomic datasets with a genome-specific marker database and with a comprehensive antibiotic resistance database. RESULTS: In the four patients, the metagenomic approach identified between eight and 11 pathogen classes that potentially cause digestive disorders. For bacterial pathogens, the diagnostic agreement between multiplex PCR and metagenomics was high; yet, metagenomics diagnosed several bacteria not detected by multiplex PCR. In contrast, some of the helminth and intestinal protozoa infections detected by microscopy were missed by metagenomics. The antimicrobial resistance analysis revealed the presence of genes conferring resistance to several commonly used antibiotics. CONCLUSIONS: A metagenomic approach provides detailed information on the presence and diversity of pathogenic organisms in human stool samples. Metagenomic studies allow for in-depth molecular characterization such as the antimicrobial resistance status, which may be useful to develop setting-specific treatment algorithms. While metagenomic approaches remain challenging, the benefits of gaining new insights into intestinal microbial communities call for a broader application in epidemiologic studies. TRIAL REGISTRATION: ISRCTN86951400.201626391184
581720.9997Comparative genomics reveals the correlations of stress response genes and bacteriophages in developing antibiotic resistance of Staphylococcus saprophyticus. Staphylococcus saprophyticus is the second most common bacteria associated with urinary tract infections (UTIs) in women. The antimicrobial treatment regimen for uncomplicated UTI is normally nitrofurantoin, trimethoprim-sulfamethoxazole (TMP-SMX), or a fluoroquinolone without routine susceptibility testing of S. saprophyticus recovered from urine specimens. However, TMP-SMX-resistant S. saprophyticus has been detected recently in UTI patients, as well as in our cohort. Herein, we investigated the understudied resistance patterns of this pathogenic species by linking genomic antibiotic resistance gene (ARG) content to susceptibility phenotypes. We describe ARG associations with known and novel SCCmec configurations as well as phage elements in S. saprophyticus, which may serve as intervention or diagnostic targets to limit resistance transmission. Our analyses yielded a comprehensive database of phenotypic data associated with the ARG sequence in clinical S. saprophyticus isolates, which will be crucial for resistance surveillance and prediction to enable precise diagnosis and effective treatment of S. saprophyticus UTIs.202338051037
340530.9997Practical implications of erythromycin resistance gene diversity on surveillance and monitoring of resistance. Use of antibiotics in human and animal medicine has applied selective pressure for the global dissemination of antibiotic-resistant bacteria. Therefore, it is of interest to develop strategies to mitigate the continued amplification and transmission of resistance genes in environmental reservoirs such as farms, hospitals and watersheds. However, the efficacy of mitigation strategies is difficult to evaluate because it is unclear which resistance genes are important to monitor, and which primers to use to detect those genes. Here, we evaluated the diversity of one type of macrolide antibiotic resistance gene (erm) in one type of environment (manure) to determine which primers would be most informative to use in a mitigation study of that environment. We analyzed all known erm genes and assessed the ability of previously published erm primers to detect the diversity. The results showed that all known erm resistance genes group into 66 clusters, and 25 of these clusters (40%) can be targeted with primers found in the literature. These primers can target 74%-85% of the erm gene diversity in the manures analyzed.201829346541
465340.9997Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints. Current surveillance of antimicrobial resistance (AMR) is mostly based on testing indicator bacteria using minimum inhibitory concentration (MIC) panels. Metagenomics has the potential to identify all known antimicrobial resistant genes (ARGs) in complex samples and thereby detect changes in the occurrence earlier. Here, we simulate the results of an AMR surveillance program based on metagenomics in the Danish pig population. We modelled both an increase in the occurrence of ARGs and an introduction of a new ARG in a few farms and the subsequent spread to the entire population. To make the simulation realistic, the total cost of the surveillance was constrained, and the sampling schedule was set at one pool per month with 5, 20, 50, or 100 samples. Our simulations demonstrate that a pool of 20-50 samples and a sequencing depth of 250 million fragments resulted in the shortest time to detection in both scenarios, with a time delay to detection of change of [Formula: see text]15 months in all scenarios. Compared with culture-based surveillance, our simulation indicates that there are neither significant reductions nor increases in time to detect a change using metagenomics. The benefit of metagenomics is that it is possible to monitor all known resistance in one sampling and laboratory procedure in contrast to the current monitoring that is based on the phenotypic characterisation of selected indicator bacterial species. Therefore, overall changes in AMR in a population will be detected earlier using metagenomics due to the fact that the resistance gene does not have to be transferred to and expressed by an indicator bacteria before it is possible to detect.202337990114
340450.9997Association between antibiotic residues, antibiotic resistant bacteria and antibiotic resistance genes in anthropogenic wastewater - An evaluation of clinical influences. The high use of antibiotics in human and veterinary medicine has led to a wide spread of antibiotics and antimicrobial resistance into the environment. In recent years, various studies have shown that antibiotic residues, resistant bacteria and resistance genes, occur in aquatic environments and that clinical wastewater seems to be a hot spot for the environmental spread of antibiotic resistance. Here a representative statistical analysis of various sampling points is presented, containing different proportions of clinically influenced wastewater. The statistical analysis contains the calculation of the odds ratios for any combination of antibiotics with resistant bacteria or resistance genes, respectively. The results were screened for an increased probability of detecting resistant bacteria, or resistance genes, with the simultaneous presence of antibiotic residues. Positive associated sets were then compared, with regards to the detected median concentration, at the investigated sampling points. All results show that the sampling points with the highest proportion of clinical wastewater always form a distinct cluster concerning resistance. The results shown in this study lead to the assumption that ciprofloxacin is a good indicator of the presence of multidrug resistant P. aeruginosa and extended spectrum β-lactamase (ESBL)-producing Klebsiella spec., Enterobacter spec. and Citrobacter spec., as it positively relates with both parameters. Furthermore, a precise relationship between carbapenemase genes and meropenem, regarding the respective sampling sites, could be obtained. These results highlight the role of clinical wastewater for the dissemination and development of multidrug resistance.202031622887
193360.9997Antibiotic Resistance Genes Occurrence in Conventional and Antibiotic-Free Poultry Farming, Italy. Antimicrobial resistance is a complex and widespread problem threatening human and animal health. In poultry farms, a wide distribution of resistant bacteria and their relative genes is described worldwide, including in Italy. In this paper, a comparison of resistance gene distribution in litter samples, recovered from four conventional and four antibiotic-free broiler flocks, was performed to highlight any influence of farming systems on the spreading and maintenance of resistance determinants. Conventional PCR tests, targeting the resistance genes related to the most used antibiotics in poultry farming, along with some critically important antibiotics for human medicine, were applied. In conventional farms, n. 10 out of n. 30 investigated genes were present in at least one sample, the most abundant fragments being the tet genes specific for tetracyclines, followed by those for aminoglycosides and chloramphenicol. All conventional samples resulted negative for colistin, carbapenems, and vancomycin resistance genes. A similar trend was observed for antibiotic-free herds, with n. 13 out of n. 30 amplified genes, while a positivity for the mcr-1 gene, specific for colistin, was observed in one antibiotic-free flock. The statistical analysis revealed a significant difference for the tetM gene, which was found more frequently in the antibiotic-free category. The analysis carried out in this study allowed us to obtain new data about the distribution of resistance patterns in the poultry industry in relation to farming types. The PCR test is a quick and non-expensive laboratory tool for the environmental monitoring of resistance determinants identifying potential indicators of AMR dissemination.202236139170
493670.9997A New Tool for Analyses of Whole Genome Sequences Reveals Dissemination of Specific Strains of Vancomycin-Resistant Enterococcus faecium in a Hospital. A new easy-to-use online bioinformatic tool analyzing whole genome sequences of healthcare associated bacteria was used by a local infection control unit to retrospectively map genetic relationship of isolates of E. faecium carrying resistance genes to vancomycin in a hospital. Three clusters of isolates were detected over a period of 5 years, suggesting transmission between patients. Individual relatedness between isolates within each cluster was established by SNP analyses provided by the system. Genetic antimicrobial resistance mechanisms to antibiotics other than vancomycin were identified. The results suggest that the system is suited for hospital surveillance of E. faecium carrying resistance genes to vancomycin in settings with access to next Generation Sequencing without bioinformatic expertise for interpretation of the genome sequences.202134778297
393480.9997Prevalence of antimicrobial resistance genes and its association with restricted antimicrobial use in food-producing animals: a systematic review and meta-analysis. BACKGROUND: There is ongoing debate regarding potential associations between restrictions of antimicrobial use and prevalence of antimicrobial resistance (AMR) in bacteria. OBJECTIVES: To summarize the effects of interventions reducing antimicrobial use in food-producing animals on the prevalence of AMR genes (ARGs) in bacteria from animals and humans. METHODS: We published a full systematic review of restrictions of antimicrobials in food-producing animals and their associations with AMR in bacteria. Herein, we focus on studies reporting on the association between restricted antimicrobial use and prevalence of ARGs. We used multilevel mixed-effects models and a semi-quantitative approach based on forest plots to summarize findings from studies. RESULTS: A positive effect of intervention [reduction in prevalence or number of ARGs in group(s) with restricted antimicrobial use] was reported from 29 studies for at least one ARG. We detected significant associations between a ban on avoparcin and diminished presence of the vanA gene in samples from animals and humans, whereas for the mecA gene, studies agreed on a positive effect of intervention in samples only from animals. Comparisons involving mcr-1, blaCTX-M, aadA2, vat(E), sul2, dfrA5, dfrA13, tet(E) and tet(P) indicated a reduced prevalence of genes in intervention groups. Conversely, no effects were detected for β-lactamases other than blaCTX-M and the remaining tet genes. CONCLUSIONS: The available body of scientific evidence supported that restricted use of antimicrobials in food animals was associated with an either lower or equal presence of ARGs in bacteria, with effects dependent on ARG, host species and restricted drug.202133146719
340290.9997Antibiotic resistance, virulence factors and biofilm formation ability in Escherichia coli strains isolated from chicken meat and wildlife in the Czech Republic. Attachment of pathogenic bacteria to food contact surfaces and the subsequent biofilm formation represent a serious threat for the food industry, since these bacteria are more resistant to antimicrobials or possess more virulence factors. The main aim of this study was to investigate the correlation between antibiotic resistance against 13 antibiotics, distribution of 10 virulence factors and biofilm formation in 105 Escherichia coli strains according to their origin. The high prevalence of antibiotic resistance that we have found in wildlife isolates could be acquired by horizontal transfer of resistance genes from human or domestic or farm animals. Consequently, these commensal bacteria might serve as indicator of antimicrobial usage for human and veterinary purposes in the Czech Republic. Further, 46 out of 66 resistant isolates (70%) were able to form biofilm and we found out statistically significant correlation between prevalence of antibiotic resistance and biofilm formation ability. The highest prevalence of antibiotic resistance was observed in weak biofilm producers. Biofilm formation was not statistically associated with any virulence determinant. However, we confirmed the correlation between prevalence of virulence factors and host origin. Chicken isolates possessed more virulence factors (66%), than isolates from wildlife (37%). We can conclude that the potential spread of antibiotic resistance pattern via the food chain is of high concern for public health. Even more, alarming is that E. coli isolates remain pathogenic potential with ability to form biofilm and these bacteria may persist during food processing and consequently lead to greater risks of food contamination.201728494209
2560100.9997Metagenomic Characterization of Poultry Cloacal and Oropharyngeal Swabs in Kenya Reveals Bacterial Pathogens and Their Antimicrobial Resistance Genes. Poultry enteric bacterial diseases are of significant economic importance because they are responsible for production losses due to weight loss, increased morbidity and mortality, and increased cost of production arising from poor feed conversion and treatment. This cross-sectional purposive study characterized enteric bacterial pathogens in poultry from selected agroclimatic regions in Kenya and investigated their antimicrobial resistance gene profiles. Cloacal (n = 563) and oropharyngeal (n = 394) swabs were collected and pooled into 16 and 14 samples, respectively, to characterize bacterial pathogens and their antimicrobial resistance gene profiles. We report that Proteobacteria, Chlamydiae, and Firmicutes are the most dominant phyla present in both cloacal and oropharyngeal swabs of the six poultry species studied, indicating the colonization of the poultry gut by many pathogenic bacteria. Using KEGG and COG databases, some pathways related to metabolism, genetic information, and cellular processing were detected. We also report the abundance of antimicrobial resistance genes that confer resistance to β-lactamases, aminoglycosides, and tetracycline in most of the poultry analyzed, raising concern about the dangers associated with continuous and inappropriate use of these antibiotics in poultry production. The antimicrobial resistance gene data generated in this study provides a valuable indicator of the use of antimicrobials in poultry in Kenya. The information generated is essential for managing bacterial diseases, especially in backyard poultry raised under scavenging conditions.202438374958
3406110.9997Environmental and Pathogenic Carbapenem Resistant Bacteria Isolated from a Wastewater Treatment Plant Harbour Distinct Antibiotic Resistance Mechanisms. Wastewater treatment plants are important reservoirs and sources for the dissemination of antibiotic resistance into the environment. Here, two different groups of carbapenem resistant bacteria-the potentially environmental and the potentially pathogenic-were isolated from both the wastewater influent and discharged effluent of a full-scale wastewater treatment plant and characterized by whole genome sequencing and antibiotic susceptibility testing. Among the potentially environmental isolates, there was no detection of any acquired antibiotic resistance genes, which supports the idea that their resistance mechanisms are mainly intrinsic. On the contrary, the potentially pathogenic isolates presented a broad diversity of acquired antibiotic resistance genes towards different antibiotic classes, especially β-lactams, aminoglycosides, and fluoroquinolones. All these bacteria showed multiple β-lactamase-encoding genes, some with carbapenemase activity, such as the bla(KPC)-type genes found in the Enterobacteriaceae isolates. The antibiotic susceptibility testing assays performed on these isolates also revealed that all had a multi-resistance phenotype, which indicates that the acquired resistance is their major antibiotic resistance mechanism. In conclusion, the two bacterial groups have distinct resistance mechanisms, which suggest that the antibiotic resistance in the environment can be a more complex problematic than that generally assumed.202134572700
3401120.9997Heavy metal resistance and virulence profile in Pseudomonas aeruginosa isolated from Brazilian soils. Pseudomonas aeruginosa is an opportunistic pathogen, which can have several virulence factors that confer on it the ability to cause severe, acute and chronic infections. Thus, the simultaneous occurrence of resistance to antibiotics and heavy metals associated with the presence of virulence genes is a potential threat to human health and environmental balance. This study aimed to investigate the resistance profile to heavy metals and the correlation of this phenotype of resistance to antimicrobials and to investigate the pathogenic potential of 46 P. aeruginosa isolates obtained from the soil of five Brazilian regions. The bacteria were evaluating for antimicrobial and heavy metal resistance, as well as the presence of plasmids and virulence genes. The isolates showed resistance to four different antibiotics and the majority (n = 44) had resistance to aztreonam or ticarcillin, furthermore, 32 isolates showed concomitant resistance to both of these antibiotics. A high prevalence of virulence genes was found, which highlights the pathogenic potential of the studied environmental isolates. Moreover, a high frequency of heavy metal resistance genes was also detected, however, the phenotypic results indicated that other genes and/or mechanisms should be related to heavy metal resistance.201627197940
5672130.9997Antibiotic Resistance, Biofilm Formation, and Presence of Genes Encoding Virulence Factors in Strains Isolated from the Pharmaceutical Production Environment. The spread of bacterial resistance to antibiotics affects various areas of life. The aim of this study was to assess the occurrence of Pseudomonas aeruginosa, and other bacteria mainly from orders Enterobacterales and Staphylococcus in the pharmaceutical production sites, and to characterize isolated strains in the aspects of antibiotic resistance, biofilm formation, and presence of genes encoding virulence factors. Genes encoding selected virulence factors were detected using PCR techniques. Antimicrobial susceptibility testing was applied in accordance with the EUCAST recommendations. A total of 46 P. aeruginosa strains were isolated and 85% strains showed a strong biofilm-forming ability. The qualitative identification of genes taking part in Quorum Sensing system demonstrated that over 89% of strains contained lasR and rhlI genes. An antimicrobial susceptibility testing revealed nine strains resistant to at least one antibiotic, and two isolates were the metallo-β-lactamase producers. Moreover, the majority of P. aeruginosa strains contained genes encoding various virulence factors. Presence of even low level of pathogenic microorganisms or higher level of opportunistic pathogens and their toxic metabolites might result in the production inefficiency. Therefore, the prevention of microbial contamination, effectiveness of sanitary and hygienic applied protocols, and constant microbiological monitoring of the environment are of great importance.202133513933
3937140.9997Design of a system for monitoring antimicrobial resistance in pathogenic, zoonotic and indicator bacteria from food animals. DANMAP is a Danish programme for integrated monitoring of and research on antimicrobial resistance in bacteria from food animals, food and humans. The paper describes how bacteria from broilers, pigs, and cattle are collected, as well as the procedures for data handling and presentation of results. The bacteria from animals include certain pathogens, selected so that they are representative for submissions to Danish diagnostic laboratories, as well as zoonotic bacteria (Campylobacter, Salmonella and Yersinia) and indicator bacteria (E. coli, E. faecium and E. faecalis), from samples collected at abattoirs. The latter samples are selected so that they are representative of the respective animal populations. Therefore, the apparent prevalence of antimicrobial resistance in the populations may be calculated. The isolates are identified to species level and the results of susceptibility testing are stored as continuous variables. All isolates are maintained in a strain collection so that they are available for subsequent research projects. The data handling facilities makes it possible to present results as percent resistant isolates or as the apparent prevalence of resistance in the population, or alternatively as graphical distributions of mm inhibition zones or MIC values. Computer routines have been established that make it possible to detect specific phenotypic expressions of resistance that may be of particular interest.199910783720
5674150.9997Evaluation of Resistance by Clinically Pathogenic Bacteria to Antimicrobials and Common Disinfectants in Beijing, China. BACKGROUND: Antibiotic resistance of pathogenic bacteria is well recognized among clinicians; however, studies that directly evaluate the bacterial resistance to commonly used disinfectants in clinical settings are lacking. Currently available reports focus on the resistance of single strains to single disinfectants and do not adequately examine the degree of resistance and cross-resistance to antimicrobials in the large-scale clinical use of disinfectants. METHODS: We investigated the resistance capacity to 11 antibiotics and 7 chemical disinfectants by bacterial strains collected from body fluids of patients in 10 hospitals in Beijing, China over a 1-year period. Bacterial resistance to disinfectants was tested using minimum inhibitory concentration and minimum bactericidal concentration using agar dilution methods based on commercially available reference strains. RESULTS: A total of 1,104 pathogenic strains were identified, of which 23% were Gram-positive bacteria, 74% were Gram-negative bacteria, and 3% were fungi. Overall, resistance to antibiotics for the most common strains was significantly higher than their resistance to disinfectants. The least effective antibiotics and disinfectants were aztreonam and glutaral, respectively, exhibiting the highest overall resistance rates; while amikacin and alcohol had the lowest resistance rates. Consistently, Acinetobacter baumannii exhibited the most resistance, while Escherichia coli had the least resistance for both antibiotics and disinfectants. CONCLUSIONS: Based on the pathogen spectrum for bacterial infective pathogens evaluated in this study, as well as the status quo of their resistance to antimicrobial agents and common clinical disinfectants, it is essential for healthcare professionals to pay attention not only to the standardized use of antimicrobial agents but also to the rational application of disinfectants.201830568055
2545160.9997Environmental bacterial load during surgical and ultrasound procedures in a Swedish small animal hospital. BACKGROUND: Environmental bacteria in animal healthcare facilities may constitute a risk for healthcare-associated infections (HAI). Knowledge of the bacterial microflora composition and factors influencing the environmental bacterial load can support tailored interventions to lower the risk for HAI. The aims of this study were to: (1) quantify and identify environmental bacteria in one operating room (OR) and one ultrasound room (UR) in a small animal hospital, (2) compare the bacterial load to threshold values suggested for use in human healthcare facilities, (3) characterise the genetic relationship between selected bacterial species to assess clonal dissemination, and (4) investigate factors associated with bacterial load during surgery. Settle plates were used for passive air sampling and dip slides for surface sampling. Bacteria were identified by Matrix Assisted Laser Desorption-Time Of Flight. Antimicrobial susceptibility was determined by broth microdilution. Single nucleotide polymorphism-analysis was performed to identify genetically related isolates. Linear regression was performed to analyse associations between observed explanatory factors and bacterial load. RESULTS: The bacterial load on settle plates and dip slides were low both in the OR and the UR, most of the samples were below threshold values suggested for use in human healthcare facilities. All settle plates sampled during surgery were below the threshold values suggested for use in human clean surgical procedures. Staphylococcus spp. and Micrococcus spp. were the dominating species. There was no indication of clonal relationship among the sequenced isolates. Bacteria carrying genes conveying resistance to disinfectants were revealed. Air change and compliance with hygiene routines were sufficient in the OR. No other factors possibly associated with the bacterial load were identified. CONCLUSIONS: This study presents a generally low bacterial load in the studied OR and UR, indicating a low risk of transmission of infectious agents from the clinical environment. The results show that it is possible to achieve bacterial loads below threshold values suggested for use in human healthcare facilities in ORs in small animal hospitals and thus posing a reduced risk of HAI. Bacteria carrying genes conveying resistance to disinfectants indicates that resistant bacteria can persist in the clinical environment, with increased risk for HAI.202439223628
5736170.9997Comparative Genomic Analysis and Antimicrobial Resistance Profile of Enterococcus Strains Isolated from Raw Sheep Milk. The role of Enterococcus spp. in food is debated since this group of lactic acid bacteria contains opportunistic pathogenic strains, some of which exhibit a multidrug-resistant profile. In livestock farms, the use of antibiotics is the most common practice to deal with mastitis-causing bacteria. However, the heavy usage and/or misuse of antibiotics has led to the emergence of antibiotic resistance. This study aimed to genetically and phenotypically characterize Enterococcus strains isolated from raw sheep milk. Samples were collected over one year from the bulk tank of a dairy sheep farm and cultured on selective media. Isolates were purified and analyzed by whole-genome sequencing and antimicrobial susceptibility testing. The isolates were divided into clusters and the corresponding species were identified along with their genes related to virulence and antibiotic resistance. The pan-, core- and accessory-genomes of the strains were determined. Finally, the antibiotic-resistant profile of selected strains was examined and associated with their genomic characterization. These findings contribute to a better understanding of Enterococci epidemiology, providing comprehensive profiles of their virulence and resistance genes. The presence of antibiotic-resistant bacteria in raw sheep milk destined for the production of cheese should raise awareness.202540872636
5746180.9997Identification of a Novel Plasmid-Borne Gentamicin Resistance Gene in Nontyphoidal Salmonella Isolated from Retail Turkey. The spread of antibiotic-resistant bacteria presents a global health challenge. Efficient surveillance of bacteria harboring antibiotic resistance genes (ARGs) is a critical aspect to controlling the spread. Increased access to microbial genomic data from many diverse populations informs this surveillance but only when functional ARGs are identifiable within the data set. Current, homology-based approaches are effective at identifying the majority of ARGs within given clinical and nonclinical data sets for several pathogens, yet there are still some whose identities remain elusive. By coupling phenotypic profiling with genotypic data, these unknown ARGs can be identified to strengthen homology-based searches. To prove the efficacy and feasibility of this approach, a published data set from the U.S. National Antimicrobial Resistance Monitoring System (NARMS), for which the phenotypic and genotypic data of 640 Salmonella isolates are available, was subjected to this analysis. Six isolates recovered from the NARMS retail meat program between 2011 and 2013 were identified previously as phenotypically resistant to gentamicin but contained no known gentamicin resistance gene. Using the phenotypic and genotypic data, a comparative genomics approach was employed to identify the gene responsible for the observed resistance in all six of the isolates. This gene, grdA, is harbored on a 9,016-bp plasmid that is transferrable to Escherichia coli, confers gentamicin resistance to E. coli, and has never before been reported to confer gentamicin resistance. Bioinformatic analysis of the encoded protein suggests an ATP binding motif. This work demonstrates the advantages associated with coupling genomics technologies with phenotypic data for novel ARG identification.202032816720
3400190.9997Chicken liver is a potential reservoir of bacteriophages and phage-derived particles containing antibiotic resistance genes. Poultry meat production is one of the most important agri-food industries in the world. The selective pressure exerted by widespread prophylactic or therapeutic use of antibiotics in intensive chicken farming favours the development of drug resistance in bacterial populations. Chicken liver, closely connected with the intestinal tract, has been directly involved in food-borne infections and found to be contaminated with pathogenic bacteria, including Campylobacter and Salmonella. In this study, 74 chicken livers, divided into sterile and non-sterile groups, were analysed, not only for microbial indicators but also for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Both bacteria and phages were detected in liver tissues, including those dissected under sterile conditions. The phages were able to infect Escherichia coli and showed a Siphovirus morphology. The chicken livers contained from 10(3) to 10(6) phage particles per g, which carried a range of ARGs (bla(TEM) , bla(CTx-M-1) , sul1, qnrA, armA and tetW) detected by qPCR. The presence of phages in chicken liver, mostly infecting E. coli, was confirmed by metagenomic analysis, although this technique was not sufficiently sensitive to identify ARGs. In addition, ARG-carrying phages were detected in chicken faeces by qPCR in a previous study of the group. Comparison of the viromes of faeces and liver showed a strong coincidence of species, which suggests that the phages found in the liver originate in faeces. These findings suggests that phages, like bacteria, can translocate from the gut to the liver, which may therefore constitute a potential reservoir of antibiotic resistance genes.202235485188