Draft Genome Sequence of Staphylococcus gallinarum DSM 20610
            <sup>T</sup>
            , Originally Isolated from the Skin of a Chicken

Shi, Ding; Fang, Daiqiong; Hu, Xinjun; Li, Ang; Lv, Longxian; Guo, Jing; Chen, Yanfei; Wu, Wenrui; Guo, Feifei

doi:10.1128/genomea.00580-15

Cited by 7 publications

(4 citation statements)

References 16 publications

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“…Some extreme cases were observed, such as streptogramins resistance for S. gallinarum , erythromycin resistance in S. cohnii , and erythromycin and penicillin resistance for S. arlettae . It is noteworthy that S. gallinarum is frequently isolated from poultry (Shi et al, 2015 ) but only occasionally infects dairy cows. In Canada, virginiamycin is used in poultry for growth promotion and prevention of infectious diseases.…”

Section: Discussionmentioning

confidence: 99%

Prevalence and Genetic Basis of Antimicrobial Resistance in Non-aureus Staphylococci Isolated from Canadian Dairy Herds

et al. 2018

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Emergence and spread of antimicrobial resistance is a major concern for the dairy industry worldwide. Objectives were to determine: (1) phenotypic and genotypic prevalence of drug-specific resistance for 25 species of non-aureus staphylococci, and (2) associations between presence of resistance determinants and antimicrobial resistance. Broth micro-dilution was used to determine resistance profiles for 1,702 isolates from 89 dairy herds. Additionally, 405 isolates were sequenced to screen for resistance determinants. Antimicrobial resistance was clearly species-dependent. Resistance to quinupristin/dalfopristin was common in Staphylococcus gallinarum (prevalence of 98%), whereas S. cohnii and S. arlettae were frequently resistant to erythromycin (prevalence of 63 and 100%, respectively). Prevalence of resistance was 10% against β-lactams and tetracyclines. In contrast, resistance to antimicrobials critically important for human medicine, namely vancomycin, fluoroquinolones, linezolid and daptomycin, was uncommon (< 1%). Genes encoding multidrug-resistance efflux pumps and resistance-associated residues in deducted amino acid sequences of the folP gene were the most frequent mechanisms of resistance, regardless of species. The estimated prevalence of the mecA gene was 17% for S. epidermidis. Several genes, including blaZ, mecA, fexA, erm, mphC, msrA, and tet were associated with drug-specific resistance, whereas other elements were not. There were specific residues in gyrB for all isolates of species intrinsically resistant to novobiocin. This study provided consensus protein sequences of key elements previously associated with resistance for 25 species of non-aureus staphylococci from dairy cattle. These results will be important for evaluating effects of interventions in antimicrobial use in Canadian dairy herds.

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Section: Discussionmentioning

confidence: 99%

Prevalence and Genetic Basis of Antimicrobial Resistance in Non-aureus Staphylococci Isolated from Canadian Dairy Herds

et al. 2018

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“…S. gallinarum spp. are opportunistic human pathogens that have primarily been identified in poultry (Shi et al, 2015 ). S. warneri was detected as an endophyte in the peel of apples from major commercial markets in Tamil Nadu, India (Phukon et al, 2013 ).…”

Section: Resultsmentioning

confidence: 99%

Microbiota and its antibiotic resistance profile in avocado Guatemalan fruits (Persea nubigena var. guatemalensis) sold at retail markets of Ibarra city, northern Ecuador

Angamarca,

Castillejo,

Tenea

2023

Front. Microbiol.

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IntroductionAvocados are typically sold in unsanitary conditions at the retail markets in Ecuador, which can raise the risk of microbial contamination. These microorganisms could exhibit multi-antibiotic resistance (MAR), being a serious threat concern to human health. In this study, we aimed to evaluate the microbiota and its antibiotic resistance profile in avocado Guatemalan fruits (Persea nubigena var. guatemalensis), at ripe stage: immature, firm light green (ready to eat in 4 days), peel (AFPE) and pulp (AFPU), and mature intense green (ready to eat) peel (AMPE) and pulp (AMPU), to gain baseline information on the prevalence of MAR bacteria.MethodsCulture-independent (16S rRNA metagenomics) and culture-dependent approach (to detect specific indicator microorganisms) were used. Moreover, antibiotic susceptibility of selected target indicator bacteria was assessed providing information about the antibiotic resistance (AR) among the groups.ResultsBased on 16S rRNA gene metagenomic analysis, over 99.78% of reads were classified as bacteria in all samples. Shannon diversity index varies from 1.22 to 2.22, with the highest bacterial population assigned to AFPE samples (1327 species). The highest microbial counts of indicator Staphylococcus spp. (STAPHY), Enterobacter spp. (ENT), and Listeria spp. (LIST), were detected in AMPE samples. Thirty percent of the selected STAPHYs, and 20.91% of Enterobacter (ENT) clones were resistant to various classes of antibiotics. The MAR index varies between 0.25 to 0.88 and was clone-, and fruit ripe stage-dependent.ConclusionsThe results indicated that ready to eat avocados contained detectable levels of MAR bacteria, including methicillin resistant (MR)-STAPHY, which may act as a potential vector for the spread of antibiotic resistance. To achieve the increase of the production and marketing of Fuerte cultivar in Ecuador, it is vitally important to consider valuable strategies to protect the fruits at the early ripe stage in future. Thus, it is crucial to set up efficient control measures and develop coordinated strategies to guarantee the microbiological quality of the food.

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“…The dDDH values were calculated using the web-based genome-to-genome distance calculator (GGDC) version 2.1 (71), and the recommended formula 2 was taken into account to interpret the results. Whole-genome sequences of related staphylococcal species were obtained from the NCBI database (72)(73)(74)(75).…”

Section: Methodsmentioning

confidence: 99%

Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments

Pantůček

Sedláček

Indráková

et al. 2018

Appl Environ Microbiol

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Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources, stone fragments and sandy soil in James Ross Island, Antarctica. Here we describe properties of novel species of the genus that has near identical 16S rRNA gene sequence to However, compared to and the next closest relatives, the new species demonstrates considerable phylogenetic distance at whole genome level, average nucleotide identity<85 %, and inferred DNA-DNA hybridization <30%. It forms a separate branch in phylogenetic clade confirmed by multilocus sequence analysis of six housekeeping genes, ,, ,, and MALDI-TOF MS and key biochemical characteristics allowed these bacteria to be distinguished from their nearest phylogenetic neighbours. In contrast to subsp. , strains were pyrrolidonyl arylamidase- and β-glucuronidase-positive, β -galactosidase-negative, nitrate was reduced and acid produced aerobically from d-mannose. Whole genome sequencing of 2.75 Mb large chromosome revealed the presence of a number of mobile genetic elements including the 27-kb-long pseudo staphylococcus cassette chromosome (ψSCC) harboring gene, two composite phage-inducible chromosomal islands probably essential to adaptation to extreme environment, and one complete and one defective prophage. Both strains are resistant to penicillin G, ampicillin, ceftazidin, methicillin, cefoxitin, and fosfomycin. We hypothesize that antibiotic resistance might represent an evolutionary advantage against beta-lactams producers, which are common in a polar environment. Based on these results, a novel species of the genus is described and named sp. nov. The type strain is P5085 (=CCM 8730 = DSM 104441). The description of sp. nov. enables the comparison of multidrug-resistant staphylococci from human and veterinary sources evolved in the globalized world to their geographically distant relative from the extreme Antarctic environment. Although this new species was not exposed to the pressure of antibiotic treatment in human or veterinary practice, mobile genetic elements carrying antimicrobial resistance genes were found in the genome. The presented genomic characteristics elucidate the evolutionary relationships in the genus with a special focus on antimicrobial resistance, pathogenicity and survival traits. Genes encoded on mobile genetic elements were arranged in unique combinations but retained conserved locations for the integration of mobile genetic elements. These findings point to enormous plasticity of the staphylococcal pangenome shaped by horizontal gene transfer. Thus can act not only as a reservoir of antibiotic resistance in a natural environment, but also as a mediator for the spread and evolution of resistance genes.

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Draft Genome Sequence of Staphylococcus gallinarum DSM 20610 ^T , Originally Isolated from the Skin of a Chicken

Cited by 7 publications

References 16 publications

Prevalence and Genetic Basis of Antimicrobial Resistance in Non-aureus Staphylococci Isolated from Canadian Dairy Herds

Prevalence and Genetic Basis of Antimicrobial Resistance in Non-aureus Staphylococci Isolated from Canadian Dairy Herds

Microbiota and its antibiotic resistance profile in avocado Guatemalan fruits (Persea nubigena var. guatemalensis) sold at retail markets of Ibarra city, northern Ecuador

Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments

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Draft Genome Sequence of Staphylococcus gallinarum DSM 20610 T , Originally Isolated from the Skin of a Chicken

Cited by 7 publications

References 16 publications

Prevalence and Genetic Basis of Antimicrobial Resistance in Non-aureus Staphylococci Isolated from Canadian Dairy Herds

Prevalence and Genetic Basis of Antimicrobial Resistance in Non-aureus Staphylococci Isolated from Canadian Dairy Herds

Microbiota and its antibiotic resistance profile in avocado Guatemalan fruits (Persea nubigena var. guatemalensis) sold at retail markets of Ibarra city, northern Ecuador

Staphylococcus edaphicus sp. nov., Isolated in Antarctica, Harbors the mecC Gene and Genomic Islands with a Suspected Role in Adaptation to Extreme Environments

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Draft Genome Sequence of Staphylococcus gallinarum DSM 20610 ^T , Originally Isolated from the Skin of a Chicken