# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 5500 | 0 | 0.9993 | Whole genome sequence analyses-based assessment of virulence potential and antimicrobial susceptibilities and resistance of Enterococcus faecium strains isolated from commercial swine and cattle probiotic products. Enterococcus faecium is one of the more commonly used bacterial species as a probiotic in animals. The organism, a common inhabitant of the gut of animals and humans, is a major nosocomial pathogen responsible for a variety infections in humans and sporadic infections in animals. In swine and cattle, E. faecium-based probiotic products are used for growth promotion and gut functional and health benefits. The objective of this study was to utilize whole genome sequence-based analysis to assess virulence potential, detect antimicrobial resistance genes, and analyze phylogenetic relationships of E. faecium strains from commercial swine and cattle probiotics. Genomic DNA extracted from E. faecium strains, isolated from commercial probiotic products of swine (n = 9) and cattle (n = 13), were sequenced in an Illumina MiSeq platform and analyzed. Seven of the nine swine strains and seven of the 13 cattle strains were identified as Enterococcus lactis, and not as E. faecium. None of the 22 probiotic strains carried major virulence genes required to initiate infections, but many carried genes involved in adhesion to host cells, which may benefit the probiotic strains to colonize and persist in the gut. Strains also carried genes encoding resistance to a few medically important antibiotics, which included aminoglycosides [aac(6')-Ii, aph(3')-III, ant(6)-Ia], macrolide, lincosamide and streptogramin B (msrC), tetracyclines [tet(L) and tet(M)], and phenicols [cat-(pc194)]. The comparison of the genotypic to phentypic AMR data showed presence of both related and unrelated genes in the probiotic strains. Swine and cattle probiotic E. faecium strains belonged to diverse sequence types. Phylogenetic analysis of the probiotic strains, and strains of human (n = 29), swine (n = 4), and cattle (n = 4) origin, downloaded from GenBank, indicated close clustering of strains belonging to the same species and source, but a few swine and cattle probiotic strains clustered closely with other cattle and human fecal strains. In conclusion, the absence of major virulence genes characteristic of the clinical E. faecium strains suggests that these probiotic strains are unlikely to initiate opportunistic infection. However, the carriage of AMR genes to medically important antibiotics and close clustering of the probiotic strains with other human and cattle fecal strains suggests that probiotic strains may pose risk to serve as a source of transmitting AMR genes to other gut bacteria. | 2022 | 35150575 |
| 5811 | 1 | 0.9993 | Antimicrobial susceptibility testing and tentative epidemiological cut-off values for Lactobacillaceae family species intended for ingestion. INTRODUCTION: In this work, 170 strains covering 13 species from the Lactobacillaceae family were analyzed to determine minimal inhibitory concentration (MIC) distributions to nine antimicrobial agents, and genes potentially conferring resistance. This allows a proposal of tentative Epidemiological Cut-Offs (ECOFFs) that follows the phylogeny for interpretation of resistance in the 13 species. METHODS: The 170 strains originated from different sources, geographical areas, and time periods. MICs for nine antibiotics were determined according to the ISO 10932 standard for lactobacillia and by a modified CLSI-method for Leuconostoc and Pediococcus which ensured sufficient growth. The strains were whole genome sequenced, subtyped by core genome analysis, and assessed for the presence of antibiotic resistance genes using the ResFinder and NCBI AMRFinder databases. RESULTS AND DISCUSSION: The data provide evidence that antimicrobial susceptibility follows phylogeny instead of fermentation pattern and accordingly, tentative ECOFFs were defined. For some species the tentative ECOFFs for specific antibiotics are above the cut-off values set by the European Food Safety Authority (EFSA) which are primarily defined according to fermentation pattern or at genus level. The increased tolerance for specific antibiotics observed for some species was evaluated to be innate, as only for one strain phenotypic resistance was found to be related to an acquired resistance gene. In general, more data are needed to define ECOFFs and since the number of isolates available for industrial relevant bacterial species are often limited compared to clinically relevant species, it is important; 1) that strains are unambiguously defined at species level and subtyped through core genome analysis, 2) MIC determination are performed by use of a standardized method to define species-specific MIC distributions and 3) that known antimicrobial resistance genes are determined in whole genome sequences to support the MIC determinations. | 2023 | 39816654 |
| 6065 | 2 | 0.9993 | Screening for enterocins and detection of hemolysin and vancomycin resistance in enterococci of different origins. The inhibitory activity of 122 out of 426 Enterococcus strains of geographically widespread origin and from different sources (food and feed, animal isolates, clinical and nonclinical human isolates) was tested against a wide range of indicator bacteria. Seventy-two strains, mainly belonging to the species Enterococcus faecium and Enterococcus faecalis were bacteriocinogenic. A remarkable variation of inhibitory spectra occurred among the strains tested, including inhibition of, for instance, only closely related enterococci, other lactic acid bacteria (LAB), food spoilage and pathogenic bacteria. No correlation could be found between the origin of the strains and the type of inhibitory spectrum, although a clustering of human isolates from both fecal and clinical origin was observed in the group of strains inhibiting lactic acid bacteria, Listeria, and either Staphylococcus or Clostridium. No relationship could be established between the presence of enterocin structural genes and the origin of the strain either, and hence no correlation seemed to exist between the presence of known enterocin genes and the activity spectra of these enterococci. The structural gene of enterocin A was widely distributed among E. faecium strains, whereas that of enterocin B only occurred in the presence of enterocin A. The vancomycin resistance phenotype as well as the presence of vancomycin resistance genes was also investigated. The vanA gene only occurred among E. faecium strains. The incidence of beta-hemolysis was not restricted to E. faecalis strains, but among the E. faecium strains the structural genes of cytolysin were not detected. beta-Hemolysis occurred in strains both from food and nonfood origin. It has been concluded that bacteriocin-producing E. faecium strains lacking hemolytic activity and not carrying cytolysin nor vancomycin resistance genes may be useful as starter cultures, cocultures, or probiotics. | 2003 | 12810293 |
| 5810 | 3 | 0.9992 | Evolutionary conservation of motifs within vanA and vanB of vancomycin-resistant enterococci. BACKGROUND AND AIM: Global Health is threatened by the rapid emergence of multidrug-resistant bacteria. Antibiotic resistomes rapidly evolve, yet conserved motifs elucidated in our study have the potential for future drug targets for precision medicine. This study aimed to identify conserved genetic sequences and their evolutionary pathways among vancomycin-resistant Enterococcus species such as Enterococcus faecium and Enterococcus faecalis. MATERIALS AND METHODS: We retrieved a total of 26 complete amino acid and nucleotide sequences of resistance determinant genes against vancomycin (vanA and vanB), streptomycin (aac-aah), and penicillin (pbp5) from the publicly available genetic sequence database, GenBank. The sequences were comprised of bacteria classified under the genera of Enterococcus, Staphylococcus, Amycolatopsis, Ruminococcus, and Clostridium. Sequences were aligned with Clustal Omega Multiple Sequence Alignment program and Percent Identity Matrices were derived. Phylogenetic analyses to elucidate evolutionary relationships between sequences were conducted with the neighbor-end joining method through the Molecular Evolutionary Genetics Analysis (MEGAX) software, developed by the Institute of Molecular Evolutionary Genetics at Pennsylvania State University. Subsequent network analyses of the resistance gene, vanB, within E. faecium were derived from ScanProsite and InterPro. RESULTS: We observed the highest nucleotide sequence similarity of vanA regions within strains of E. faecium (100%) and E. faecalis (100%). Between Enterococcus genera, we continued to observe high sequence conservation for vanA and vanB, up to 99.9% similarity. Phylogenetic tree analyses suggest rapid acquisition of these determinants between strains within vanA and vanB, particularly between strains of Enterococcus genera, which may be indicative of horizontal gene transfer. Within E. faecium, Adenosine 5'-Triphosphate (ATP)-Grasp and D-ala-D-ala ligase (Ddl) were found as conserved domains of vanA and vanB. We additionally found that there is notable sequence conservation, up to 66.67%, between resistomes against vancomycin and streptomycin among E. faecium. CONCLUSION: Resistance genes against vancomycin have highly conserved sequences between strains of Enterococcus bacteria. These conserved sequences within vanA and vanB encode for ATP-Grasp and Ddl motifs, which have functional properties for maintaining cell wall integrity. High sequence conservation is also observed among resistance genes against penicillin and streptomycin, which can inform future drug targets for broader spectrum therapies. | 2022 | 36425127 |
| 5501 | 4 | 0.9992 | The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential. This study aimed to characterize the species, antimicrobial resistance and dispersion of CRISPR systems in staphylococci isolated from the oropharynx of domestic cats in Brazil. Staphylococcus strains (n=75) were identified by MALDI-TOF and sequencing of rpoB and tuf genes. Antimicrobial susceptibility was assessed by disk diffusion method and PCR to investigate the presence of antimicrobial-resistance genes usually present in mobile genetic elements (plasmids), in addition to plasmid extraction. CRISPR - genetic arrangements that give the bacteria the ability to resist the entry of exogenous DNA - were investigated by the presence of the essential protein Cas1 gene. A great diversity of Staphylococcus species (n=13) was identified. The presence of understudied species, like S. nepalensis and S. pettenkoferi reveals that more than one identification method may be necessary to achieve conclusive results. At least 56% of the strains contain plamids, being 99% resistant to at least one of the eight tested antimicrobials and 12% multidrug resistant. CRISPR were rare among the studied strains, consistent with their putative role as gene reservoirs. Moreover, herein we describe for the first time their existence in Staphylococcus lentus, to which the system must confer additional adaptive advantage. Prevalence of resistance among staphylococci against antimicrobials used in veterinary and human clinical practice and the zoonotic risk highlight the need of better antimicrobial management practices, as staphylococci may transfer resistance genes among themselves, including to virulent species, like S. aureus. | 2017 | 28284599 |
| 5734 | 5 | 0.9992 | Escherichia coli Strains Originating from Raw Sheep Milk, with Special Reference to Their Genomic Characterization, Such as Virulence Factors (VFs) and Antimicrobial Resistance (AMR) Genes, Using Whole-Genome Sequencing (WGS). The objective of this work was to deliver a comprehensive genetic characterization of a collection of E. coli strains isolated from raw sheep milk. To complete our purpose, the technique of whole-genome sequencing, coupled with bioinformatics and phenotypic characterization of antimicrobial resistance, was performed. These Gram-negative, facultative anaerobic bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Shigella spp. and Salmonella spp. Genetic analysis was carried out on all strains (phylogram, sequence types, VFs, AMR genes, and pangenome). The results showed the presence of various genetic traits that are related to virulence factors contributing to their pathogenic potential. In addition, genes conferring resistance to antibiotics were also detected and confirmed using phenotypic tests. Finally, the genome of the E. coli strains was characterized by the presence of several mobile genetic elements, thus facilitating the exchange of various genetic elements, associated with virulence and antimicrobial resistance, within and beyond the species, through horizontal gene transfer. Contaminated raw sheep milk with pathogenic E. coli strains is particularly alarming for cheese production in artisan dairies. | 2025 | 40872695 |
| 4600 | 6 | 0.9992 | The ecological importance of the Staphylococcus sciuri species group as a reservoir for resistance and virulence genes. The Staphylococcus sciuri species group includes five species that are most often presented as commensal animal-associated bacteria. The species of this group are Staphylococcus sciuri (with three subspecies), Staphylococcus lentus, Staphylococcus vitulinus, Staphylococcus fleurettii and Staphylococcus stepanovicii. Members of these group are commonly found in a broad range of habitats including animals, humans and the environment. However, those species have been isolated also from infections, both in veterinary and human medicine. Members of this group have been shown to be pathogenic, though infections caused by these species are infrequent. Furthermore, members of the S. sciuri species group have also been found to carry multiple virulence and resistance genes. Indeed, genes implicated in biofilm formation or coding for toxins responsible of toxic shock syndrome and multi-resistance, similar to those carried by Staphylococcus aureus, were detected. This group may thereby represent a reservoir for other bacteria. Despite its recognized abundance as commensal bacteria and its possible role as reservoir of virulence and resistance genes for other staphylococci, the S. sciuri species group is often considered harmless and, as such, not as well documented as, for example, S. aureus. More investigation into the role of the S. sciuri species group as commensal and pathogenic bacteria is required to fully assess its medical and veterinary importance. | 2014 | 24629775 |
| 4685 | 7 | 0.9992 | Antimicrobial Susceptibility Profile and Whole-Genome Analysis of a Strong Biofilm-Forming Bacillus Sp. B87 Strain Isolated from Food. Members of the Bacillus cereus group are considered to be foodborne pathogens commonly associated with diarrheal and emetic gastrointestinal syndromes. Biofilm formation is a major virulence determinant of various pathogenic bacteria, including the B. cereus strains, since it can protect the bacteria against antimicrobial agents and the host immune response. Moreover, a biofilm allows the exchange of genetic material, such as antimicrobial resistance genes, among the different bacterial strains inside the matrix. The aim of the current study was to genotypically and phenotypically characterize Bacillus sp. B87, a strain that was isolated from food and which exhibited strong biofilm-forming capacity. Based on the analysis of the phylogenetic relationship, the isolate was phylogenetically mapped close to Bacillus pacificus. Antimicrobial susceptibility testing revealed that the isolate was resistant to tetracycline and β-lactam antimicrobial agents, which corresponded with the genotypic characterization using the whole-genome analysis. The genome of Bacillus sp. B87 carried the three-component non-hemolytic enterotoxin (NHE), which is a type of enterotoxin that causes diarrheal symptoms. In addition, the genome also contained several genes that participate in biofilm formation, including the pelDEA(DA)FG operon. These findings expand our understanding of antimicrobial resistance and virulence in Bacillus species based on the link between genotypic and phenotypic characterization. | 2022 | 35208707 |
| 4928 | 8 | 0.9992 | Whole genome sequencing data of Klebsiella aerogenes isolated from agricultural soil of Haryana, India. Klebsiella aerogenes, is a Gram-negative bacterium, which was previously known as Enterobacter aerogenes. It is present in all environments such as water, soil, air and hospitals; and is an opportunistic pathogen that causes several types of infections. As compared to other clinically important pathogens included in the ESKAPE category (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), the pangenome and population structure of Klebsiella aerogenes is still poorly understood. For the present study, the bacterial sample was isolated from agricultural soils of Haryana, India. With an aim to identify the occurrence of multi-drug resistance genes in the agricultural field soil bacterial isolate, whole genome sequencing (WGS) of the bacteria was performed; and the antibiotic resistance causing genes, along with the genes responsible for other major functions of the cell; and the different Single Nuceotide Polymorphisms (SNPs) and Insertions and deletions (InDels) were identified. The data presented in this manuscript can be reused by researchers as a reference for determining the antibiotic resistance genes that could be present in different bacterial isolates, and it would also help in determination of functions of various other genes present in other genomes of Klebsiella species. | 2021 | 34485641 |
| 5504 | 9 | 0.9992 | Whole Genome Sequencing of Staphylococci Isolated From Bovine Milk Samples. Staphylococci are among the commonly isolated bacteria from intramammary infections in bovines, where Staphylococcus aureus is the most studied species. This species carries a variety of virulence genes, contributing to bacterial survival and spread. Less is known about non-aureus staphylococci (NAS) and their range of virulence genes and mechanisms, but they are the most frequently isolated bacteria from bovine milk. Staphylococci can also carry a range of antimicrobial resistance genes, complicating treatment of the infections they cause. We used Illumina sequencing to whole genome sequence 93 staphylococcal isolates selected from a collection of staphylococcal isolates; 45 S. aureus isolates and 48 NAS isolates from 16 different species, determining their content of antimicrobial resistance genes and virulence genes. Antimicrobial resistance genes were frequently observed in the NAS species as a group compared to S. aureus. However, the lincosamide resistance gene lnuA and penicillin resistance gene blaZ were frequently identified in NAS, as well as a small number of S. aureus. The erm genes conferring macrolide resistance were also identified in several NAS isolates and in a small number of S. aureus isolates. In most S. aureus isolates, no antimicrobial resistance genes were detected, but in five S. aureus isolates three to six resistance genes were identified and all five of these carried the mecA gene. Virulence genes were more frequently identified in S. aureus, which contained on average five times more virulence genes compared to NAS. Among the NAS species there were also differences in content of virulence genes, such as S. chromogenes with a higher average number of virulence genes. By determining the content of a large selection of virulence genes and antimicrobial resistance genes in S. aureus and 16 different NAS species our results contribute with knowledge regarding the genetic basis for virulence and antimicrobial resistance in bovine staphylococci, especially the less studied NAS. The results can create a broader basis for further research into the virulence mechanisms of this important group of bacteria in bovine intramammary infections. | 2021 | 34987483 |
| 4679 | 10 | 0.9992 | Antimicrobial and Phylogenomic Characterization of Bacillus cereus Group Strains Isolated from Different Food Sources in Italy. Background:Bacillus cereus is a widespread environmental Gram-positive bacterium which is especially common in soil and dust. It produces two types of toxins that cause vomiting and diarrhea. At present, foodborne outbreaks due to Bacillus cereus group bacteria (especially Bacillus cereus sensu stricto) are rising, representing a serious problem in the agri-food supply chain. Methods: In this work, we analyzed 118 strains belonging to the Bacillus cereus group, isolated from several food sources, for which in vitro and in silico antibiotic resistance assessments were performed. Results: Many strains showed intermediate susceptibility to clindamycin, erythromycin, and tetracycline, suggesting an evolving acquisition of resistance against these antibiotics. Moreover, one strain showed intermediate resistance to meropenem, an antibiotic currently used to treat infections caused by Bacillus cereus. In addition to the phenotypic antimicrobial resistance profile, all strains were screened for the presence/absence of antimicrobial genes via whole-genome sequencing. There was inconsistency between the in vitro and in silico analyses, such as in the case of vancomycin, for which different isolates harbored resistance genes but, phenotypically, the same strains were sensitive. Conclusions: This would suggest that antibiotic resistance is a complex phenomenon due to a variety of genetic, epigenetic, and biochemical mechanisms. | 2024 | 39335071 |
| 4965 | 11 | 0.9992 | Genomic Analysis Reveals the Genetic Determinants Associated With Antibiotic Resistance in the Zoonotic Pathogen Campylobacter spp. Distributed Globally. The genus Campylobacter groups 32 Gram-negative bacteria species, several being zoonotic pathogens and a major cause of human gastroenteritis worldwide. Antibiotic resistant Campylobacter is considered by the World Health Organization as a high priority pathogen for research and development of new antibiotics. Genetic elements related to antibiotic resistance in the classical C. coli and C. jejuni species, which infect humans and livestock, have been analyzed in numerous studies, mainly focused on local geographical areas. However, the presence of these resistance determinants in other Campylobacter species, as well as in C. jejuni and C. coli strains distributed globally, remains poorly studied. In this work, we analyzed the occurrence and distribution of antibiotic resistance factors in 237 Campylobacter closed genomes available in NCBI, obtained from isolates collected worldwide, in different dates, from distinct hosts and comprising 22 Campylobacter species. Our data revealed 18 distinct genetic determinants, genes or point mutations in housekeeping genes, associated with resistance to antibiotics from aminoglycosides, β-lactams, fluoroquinolones, lincosamides, macrolides, phenicols or tetracyclines classes, which are differentially distributed among the Campylobacter species tested, on chromosomes or plasmids. Three resistance determinants, the bla (OXA-493) and bla (OXA-576) genes, putatively related to β-lactams resistance, as well as the lnu(AN2) gene, putatively related to lincosamides resistance, had not been reported in Campylobacter; thus, they represent novel determinants for antibiotic resistance in Campylobacter spp., which expands the insight on the Campylobacter resistome. Interestingly, we found that some of the genetic determinants associated with antibiotic resistance are Campylobacter species-specific; e.g., the bla (OXA-493) gene and the T86V mutation in gyrA were found only in the C. lari group, whereas genes associated with aminoglycosides resistance were found only in C. jejuni and C. coli. Additional analyses revealed how are distributed the resistance and multidrug resistance Campylobacter genotypes assessed, with respect to hosts, geographical locations, and collection dates. Thus, our findings further expand the knowledge on the factors that can determine or favor the antibiotic resistance in Campylobacter species distributed globally, which can be useful to choose a suitable antibiotic treatment to control the zoonotic infections by these bacteria. | 2020 | 33042043 |
| 5972 | 12 | 0.9992 | Method of Selection of Bacteria Antibiotic Resistance Genes Based on Clustering of Similar Nucleotide Sequences. A new method for selection of bacterium antibiotic resistance genes is proposed and tested for solving the problems related to selection of primers for PCR assay. The method implies clustering of similar nucleotide sequences and selection of group primers for all genes of each cluster. Clustering of resistance genes for six groups of antibiotics (aminoglycosides, β-lactams, fluoroquinolones, glycopeptides, macrolides and lincosamides, and fusidic acid) was performed. The method was tested for 81 strains of bacteria of different genera isolated from patients (K. pneumoniae, Staphylococcus spp., S. agalactiae, E. faecalis, E. coli, and G. vaginalis). The results obtained by us are comparable to those in the selection of individual genes; this allows reducing the number of primers necessary for maximum coverage of the known antibiotic resistance genes during PCR analysis. | 2017 | 29063318 |
| 5502 | 13 | 0.9992 | Short communication: Diversity of species and transmission of antimicrobial resistance among Staphylococcus spp. isolated from goat milk. The increasing production of goat milk and its derivatives is affected by the occurrence of intramammary infections, which are highly associated with the presence of Staphylococcus species, including some with zoonotic potential. Staphylococci in general can exchange mobile genetic elements, a process that may be facilitated by the isolate's capacity of forming biofilms. In this study we identified, to the species level, Staphylococcus isolated from goat milk samples by MALDI-TOF and confirmed the identification by sequencing housekeeping genes (rrs and tuf). Eight species were identified, more than half being either Staphylococcus epidermidis or Staphylococcus lugdunensis. The isolates were shown by pulsed-field gel electrophoresis to be genetically diverse between the studied herds. Resistance to ampicillin and penicillin was widespread, and 2 Staph. epidermidis isolates contained the methicillin-resistance gene mecA. Most of the isolates that were resistant to at least 1 of the 13 antimicrobials tested harbored plasmids, one of which was demonstrated to be conjugative, being transferred from a Staph. epidermidis to a Staphylococcus aureus strain. Biofilm formation was observed in almost every isolate, which may contribute to their capacity of exchanging antimicrobial resistance genes in addition to acting as a physical barrier to the access of drugs. Our results showed that antimicrobial resistance among goat staphylococci may be emerging in a process facilitated by the exchange of mobile genetic elements between the bacteria and the establishment of biofilms, which calls for careful monitoring and more effective control therapies. | 2019 | 30928272 |
| 5975 | 14 | 0.9992 | Development of a DNA microarray to detect antimicrobial resistance genes identified in the National Center for Biotechnology Information database. To understand the mechanisms and epidemiology of antimicrobial resistance (AR), the genetic elements responsible must be identified. Due to the myriad of possible genes, a high-density genotyping technique is needed for initial screening. To achieve this, AR genes in the National Center for Biotechnology Information GenBank database were identified by their annotations and compiled into a nonredundant list of 775 genes. A DNA microarray was constructed of 70mer oligonucelotide probes designed to detect these genes encoding resistances to aminoglycosides, beta-lactams, chloramphenicols, glycopeptides, heavy metals, lincosamides, macrolides, metronidazoles, polyketides, quaternary ammonium compounds, streptogramins, sulfonamides, tetracyclines, and trimethoprims as well as resistance transfer genes. The microarray was validated with two fully sequenced control strains of Salmonella enterica: Typhimurium LT2 (sensitive) and Typhi CT18 (multidrug resistance [MDR]). All resistance genes encoded on the MDR plasmid, pHCM1, harbored by CT18 were detected in that strain, whereas no resistance genes were detected in LT2. The microarray was also tested with a variety of bacteria, including MDR Salmonella enterica serovars, Escherichia coli, Campylobacter spp., Enterococcus spp., methicillin-resistant Staphylococcus aureus, Listeria spp., and Clostridium difficile. The results presented here demonstrate that a microarray can be designed to detect virtually all AR genes found in the National Center for Biotechnology Information database, thus reducing the subsequent assays necessary to identify specific resistance gene alleles. | 2010 | 19916789 |
| 5470 | 15 | 0.9992 | Antimicrobial resistance genes, virulence markers and prophage sequences in Salmonella enterica serovar Enteritidis isolated in Tunisia using whole genome sequencing. Salmonella Enteritidis causes a major public health problem in the world. Whole genome sequencing can give us a lot of information not only about the phylogenetic relatedness of these bacteria but also in antimicrobial resistance and virulence gene predictions. In this study, we analyzed the whole genome data of 45 S. Enteritidis isolates recovered in Tunisia from different origins, human, animal, and foodborne samples. Two major lineages (A and B) were detected based on 802 SNPs differences. Among these SNPs, 493 missense SNPs were identified. A total of 349 orthologue genes mutated by one or two missense SNPs were classified in 22 functional groups with the prevalence of carbohydrate transport and metabolism group. A good correlation between genotypic antibiotic resistance profiles and phenotypic analysis were observed. Only resistant isolates carried the respective molecular resistant determinants. The investigation of virulence markers showed the distribution of 11 Salmonella pathogenicity islands (SPI) out of 23 previously described. The SPI-1 and SPI-2 genes encoding type III secretion systems were highly conserved in all isolates except one. In addition, the virulence plasmid genes were present in all isolates except two. We showed the presence of two fimbrial operons sef and ste previously considered to be specific for typhoidal Salmonella. Our collection of S. Enteritidis reveal a diversity among prophage profiles. SNPs analysis showed that missense mutations identified in fimbriae and in SPI-1 and SPI-2 genes were mostly detected in lineage B. In conclusion, WGS is a powerful application to study functional genomic determinants of S. Enteritidis such as antimicrobial resistance genes, virulence markers and prophage sequences. Further studies are needed to predict the impact of the missenses SNPs that can affect the protein functions associated with pathogenicity. | 2022 | 35909609 |
| 5471 | 16 | 0.9992 | Characterization of virulence and antimicrobial resistance genes of Aeromonas media strain SD/21-15 from marine sediments in comparison with other Aeromonas spp. Aeromonas media is a Gram-negative bacterium ubiquitously found in aquatic environments. It is a foodborne pathogen associated with diarrhea in humans and skin ulceration in fish. In this study, we used whole genome sequencing to profile all antimicrobial resistance (AMR) and virulence genes found in A. media strain SD/21-15 isolated from marine sediments in Denmark. To gain a better understanding of virulence and AMR genes found in several A. media strains, we included 24 whole genomes retrieved from the public databanks whose isolates originate from different host species and environmental samples from Asia, Europe, and North America. We also compared the virulence genes of strain SD/21-15 with A. hydrophila, A. veronii, and A. salmonicida reference strains. We detected Msh pili, tap IV pili, and lateral flagella genes responsible for expression of motility and adherence proteins in all isolates. We also found hylA, hylIII, and TSH hemolysin genes in all isolates responsible for virulence in all isolates while the aerA gene was not detected in all A. media isolates but was present in A. hydrophila, A. veronii, and A. salmonicida reference strains. In addition, we detected LuxS and mshA-Q responsible for quorum sensing and biofilm formation as well as the ferric uptake regulator (Fur), heme and siderophore genes responsible for iron acquisition in all A. media isolates. As for the secretory systems, we found all genes that form the T2SS in all isolates while only the vgrG1, vrgG3, hcp, and ats genes that form parts of the T6SS were detected in some isolates. Presence of bla (MOX-9) and bla (OXA-427) β-lactamases as well as crp and mcr genes in all isolates is suggestive that these genes were intrinsically encoded in the genomes of all A. media isolates. Finally, the presence of various transposases, integrases, recombinases, virulence, and AMR genes in the plasmids examined in this study is suggestive that A. media has the potential to transfer virulence and AMR genes to other bacteria. Overall, we anticipate these data will pave way for further studies on virulence mechanisms and the role of A. media in the spread of AMR genes. | 2022 | 36532448 |
| 4930 | 17 | 0.9992 | Whole-genome sequencing based characterization of antimicrobial resistance in Enterococcus. Whole-genome sequencing (WGS) has transformed our understanding of antimicrobial resistance, yielding new insights into the genetics underlying resistance. To date, most studies using WGS to study antimicrobial resistance have focused on gram-negative bacteria in the family Enterobacteriaceae, such as Salmonella spp. and Escherichia coli, which have well-defined resistance mechanisms. In contrast, relatively few studies have been performed on gram-positive organisms. We sequenced 197 strains of Enterococcus from various animal and food sources, including 100 Enterococcus faecium and 97 E. faecalis. From analyzing acquired resistance genes and known resistance-associated mutations, we found that resistance genotypes correlated with resistance phenotypes in 96.5% of cases for the 11 drugs investigated. Some resistances, such as those to tigecycline and daptomycin, could not be investigated due to a lack of knowledge of mechanisms underlying these phenotypes. This study showed the utility of WGS for predicting antimicrobial resistance based on genotype alone. | 2018 | 29617860 |
| 2442 | 18 | 0.9992 | Macrolide, lincosamide, and streptogramin B resistance in lipophilic Corynebacteria inhabiting healthy human skin. Corynebacteria exist as part of human skin microbiota. However, under some circumstances, they can cause opportunistic infections. The subject of the study was to examine the macrolide-lincosamide-streptogramin B (MLSB) antibiotic resistance in 99 lipophilic strains of Corynebacterium genus isolated from the skin of healthy men. Over 70% of the tested strains were resistant to erythromycin and clindamycin. All of which demonstrated a constitutive type of MLSB resistance mechanism. In all strains, there were being investigated the erm(A), erm(B), erm(C), erm(X), lin(A), msr(A), and mph(C) genes that could be responsible for the different types of resistance to marcolides, lincosamides, and streptogramin B. In all strains with the MLSB resistance phenotype, the erm(X) gene was detected. None of the other tested genes were discovered. Strains harboring the erm(X) gene were identified using a phenotypic method based on numerous biological and biochemical tests. Identification of the chosen strains was compared with the results of API Coryne, MALDI-TOF MS, and 16S rDNA sequencing methods. Only 7 out of the 23 investigated resistant strains provided successful results in all the used methods, showing that identification of this group of bacteria is still a great challenge. The MLSB resistance mechanism was common in most frequently isolated from healthy human skin Corynebacterium tuberculostearicum and Corynebacterium jeikeium strains. This represents a threat as these species are also commonly described as etiological factors of opportunistic infections. | 2014 | 24735183 |
| 5741 | 19 | 0.9992 | Multidrug-Resistant Klebsiella variicola Isolated in the Urine of Healthy Bovine Heifers, a Potential Risk as an Emerging Human Pathogen. Klebsiella variicola, a member of Klebsiella pneumoniae complex, is found to infect plants, insects, and animals and is considered an emerging pathogen in humans. While antibiotic resistance is often prevalent among K. variicola isolates from humans, this has not been thoroughly investigated in isolates from nonhuman sources. Prior evidence suggests that K. variicola can be transmitted between agricultural products as well as between animals, and the use of antibiotics in agriculture has increased antibiotic resistance in other emerging pathogens. Furthermore, in animals that contain K. variicola as a normal member of the rumen microbiota, the same bacteria can also cause infections, such as clinical mastitis in dairy cows. Here, we describe K. variicola UFMG-H9 and UFMG-H10, both isolated from the urine of healthy Gyr heifers. These two genomes represent the first isolates from the urine of cattle and exhibit greater similarity with strains from the human urinary tract than isolates from bovine fecal or milk samples. Unique to the UFMG-H9 genome is the presence of flagellar genes, the first such observation for K. variicola. Neither of the sampled animals had symptoms associated with K. variicola infection, even though genes associated with virulence and antibiotic resistance were identified in both strains. Both strains were resistant to amoxicillin, erythromycin, and vancomycin, and UFMG-H10 is resistant to fosfomycin. The observed resistances emphasize the concern regarding the emergence of this species as a human pathogen given its circulation in healthy livestock animals. IMPORTANCE Klebsiella variicola is an opportunistic pathogen in humans. It also has been associated with bovine mastitis, which can have significant economic effects. While numerous isolates have been sequenced from human infections, only 12 have been sequenced from cattle (fecal and milk samples) to date. Recently, we discovered the presence of K. variicola in the urine of two healthy heifers, the first identification of K. variicola in the bovine urinary tract and the first confirmed K. variicola isolate encoding for flagella-mediated motility. Here, we present the genome sequences and analysis of these isolates. The bovine urinary genomes are more similar to isolates from the human urinary tract than they are to other isolates from cattle, suggesting niche specialization. The presence of antibiotic resistance genes is concerning, as prior studies have found transmission between animals. These findings are important to understand the circulation of K. variicola in healthy livestock animals. | 2022 | 35416681 |