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Microorganisms Nov 2019Coagulase Negative Staphylococci (CoNS) are becoming increasingly recognized as an important cause of human and animal infections. Notwithstanding their clinical...
Coagulase Negative Staphylococci (CoNS) are becoming increasingly recognized as an important cause of human and animal infections. Notwithstanding their clinical relevance, annotation of genes potentially involved in pathogenicity and/or antibiotic resistance in the CoNS species (SAR) is currently very limited. In the current work we describe the genome of a novel methicillin resistant isolate of SAR, which we named Bari, and present a comprehensive analysis of predicted antibiotic resistance profiles and virulence determinants for all the 22 currently available SAR genomes. By comparing predicted antibiotic resistance and virulence-associated genes with those obtained from a manual selection of 148 bacterial strains belonging to 14 different species of staphylococci and to two "outgroup" species, (BS) and (MC), we derived some interesting observations concerning the types and number of antibiotic resistance-related and virulence-like genes in SAR. Interestingly, almost 50% of the putative antibiotic resistance determinants identified in this work, which include the clinically relevant , and genes, were shared among all the SAR strains herein considered (Bari included). Moreover, comparison of predicted antibiotic resistance profiles suggest that SAR is closely related to well-known pathogenic species, such as (SA) and (SE). A similar analysis of predicted virulence factors, revealed that several genes associated with pathogenesis (including, for example, , , and ), which are commonly found in the genomes of pathogenic staphylococci such as (SH) and (SS), are observed also in the SAR strains for which a genomic sequence is available. All in all, we believe that the analyses presented in the current study, by providing a consistent and comprehensive annotation of virulence and antibiotic resistance-related genes in SAR, can constitute a valuable resource for the study of molecular mechanisms of opportunistic pathogenicity in this species.
PubMed: 31752379
DOI: 10.3390/microorganisms7110580 -
MSphere 2017Whole-genome sequencing of penicillin-resistant strain SAN1670 from bovine mastitis milk revealed a novel β-lactamase operon consisting of the β-lactamase-encoding...
Whole-genome sequencing of penicillin-resistant strain SAN1670 from bovine mastitis milk revealed a novel β-lactamase operon consisting of the β-lactamase-encoding gene , the antirepressor-encoding gene , and the repressor-encoding gene . The functionality of was demonstrated by gene expression in . The operon was chromosomally located in SAN1670 and present in 10 additional unrelated strains, suggesting intrinsic penicillin resistance in . Furthermore, a GenBank search revealed more unique potential β-lactamases in species. Penicillins are an important group of antibiotics used to treat various types of infections caused by Gram-positive bacteria. So far, the gene was the only known β-lactamase gene in staphylococci. However, other putative β-lactamases were identified, and one of them was shown to be a novel functional β-lactamase encoded by in , further limiting treatment options.
PubMed: 28497118
DOI: 10.1128/mSphere.00117-17 -
International Microbiology : the... May 2023Staphylococcus arlettae is a rarely reported coagulase-negative staphylococcus (CoNS) isolated from infected humans and livestock. Observing phage-bacteria interaction...
BACKGROUND
Staphylococcus arlettae is a rarely reported coagulase-negative staphylococcus (CoNS) isolated from infected humans and livestock. Observing phage-bacteria interaction could improve the understanding of bacterial pathogenetic mechanisms, providing foundational evidence for phage therapy or phage detection. Herein, we aimed to characterise and annotate a novel bacteriophage, vB_SarS_BM31 (BM31), specific to S. arlettae. This bacteriophage was isolated from a milk sample associated with bovine mastitis and collected in the Sichuan Province, China.
RESULTS
The BM31 genome comprised a linear double-stranded DNA of 42,271 base pair in length with a G + C content of 34.59%. A total of 65 open reading frames (ORFs) were assembled from phage DNA, of which 29 were functionally annotated. These functional genes were divided into four modules: the structural, DNA packing and replication, lysis, and lysogeny modules. Holin (ORF25), lysin (ORF26), and integrase (ORF28) were located closely in the entire BM31 genome and were important for lyse or lysogeny cycle of BM31. The phage was identified as a temperate phage according to whole genome analysis and life cycle assay, with basic biological characteristics such as small burst size, short latency period, and narrow host range, consistent with the characteristics of the family Siphoviridae, subcluster B14 of the Staphylococcus bacteriophage.
CONCLUSIONS
The present isolation and characterisation of BM31 contributes to the Staphylococcus bacteriophage database and provides a theoretical foundation for its potential applications. To the best of our knowledge, BM31 is the only shared and completely reported phage against S. arlettae in the entire public database.
Topics: Animals; Cattle; Female; Humans; Sequence Analysis, DNA; DNA, Viral; Genome, Viral; Staphylococcus; Staphylococcus Phages
PubMed: 36336729
DOI: 10.1007/s10123-022-00292-3 -
Journal of Dairy Science Jul 2017Non-aureus staphylococci (NAS), the microorganisms most frequently isolated from bovine milk worldwide, are a heterogeneous group of numerous species. To establish their...
Non-aureus staphylococci (NAS), the microorganisms most frequently isolated from bovine milk worldwide, are a heterogeneous group of numerous species. To establish their importance as a group, the distribution of individual species needs to be determined. In the present study, NAS intramammary infection (IMI) was defined as a milk sample containing ≥1,000 cfu/mL in pure or mixed culture that was obtained from a cohort of cows assembled by the Canadian Bovine Mastitis Research Network. Overall, 6,213 (6.3%) of 98,233 quarter-milk samples from 5,149 cows and 20,305 udder quarters were associated with an NAS IMI. Of the 6,213 phenotypically identified NAS isolates, 5,509 (89%) were stored by the Canadian Bovine Mastitis Research Network Mastitis Pathogen Collection and characterized using partial sequencing of the rpoB housekeeping gene, confirming 5,434 isolates as NAS. Prevalence of each NAS species IMI was estimated using Bayesian models, with presence of a specific NAS species as the outcome. Overall quarter-level NAS IMI prevalence was 26%. The most prevalent species causing IMI were Staphylococcus chromogenes (13%), Staphylococcus simulans (4%), Staphylococcus haemolyticus (3%), Staphylococcus xylosus (2%), and Staphylococcus epidermidis (1%). The prevalence of NAS IMI as a group was highest in first-parity heifers and was evenly distributed throughout cows in parities ≥2. The IMI prevalence of some species such as S. chromogenes, S. simulans, and S. epidermidis differed among parities. Overall prevalence of NAS IMI was 35% at calving, decreased over the next 10 d, and then gradually increased until the end of lactation. The prevalence of S. chromogenes, Staphylococcus gallinarum, Staphylococcus cohnii, and Staphylococcus capitis was highest at calving, whereas the prevalence of S. chromogenes, S. haemolyticus, S. xylosus, and S. cohnii increased during lactation. Although the overall prevalence of NAS IMI was similar across barn types, the prevalence of S. simulans, S. xylosus, S. cohnii, Staphylococcus saprophyticus, S. capitis, and Staphylococcus arlettae IMI was higher in tiestall barns; the prevalence of S. epidermidis IMI was lowest; and the prevalence of S. chromogenes and Staphylococcus sciuri IMI was highest in bedded-pack barns. Staphylococcus simulans, S. epidermidis, S. xylosus, and S. cohnii IMI were more prevalent in herds with intermediate to high bulk milk somatic cell count (BMSCC) and S. haemolyticus IMI was more prevalent in herds with high BMSCC, whereas other common NAS species IMI were equally prevalent in all 3 BMSCC categories. Distribution of NAS species IMI differed among the 4 regions of Canada. In conclusion, distribution differed considerably among NAS species IMI; therefore, accurate identification (species level) is essential for studying NAS epidemiology.
Topics: Animals; Bayes Theorem; Canada; Cattle; Cattle Diseases; Female; Mammary Glands, Animal; Mastitis, Bovine; Milk; Pregnancy; Prevalence; Species Specificity; Staphylococcal Infections; Staphylococcus
PubMed: 28527793
DOI: 10.3168/jds.2016-12478 -
Access Microbiology 2023The human oral cavity comprises various niches such as teeth, gingiva, tongue, soft and hard palate, and various dental prostheses, all inhabited by different bacterial...
INTRODUCTION
The human oral cavity comprises various niches such as teeth, gingiva, tongue, soft and hard palate, and various dental prostheses, all inhabited by different bacterial species. Although more than 600 taxa belong to the oral cavity, identifying , an incompletely understood bacterium, has been rare.
METHODS
Three patients who underwent periodontal flap surgeries were reported with the incidental finding of associated with the intra-oral sutures placed. Environmental sampling was performed, to establish the exact source of this bacterium.
RESULTS
was isolated in three patients' intra-oral sutures. All environmental samples were negative for the presence of the bacterium.
CONCLUSION
. To this date, no studies have identified such an occurrence of with intra-oral sutures. Its identification in association with foreign materials, such as sutures, can be considered a potential for surgical site infections and requires further investigation.
PubMed: 37691839
DOI: 10.1099/acmi.0.000555.v4 -
Brazilian Journal of Microbiology :... Dec 2022This research aimed to identify the diversity of bacterial species of the genus Staphylococcus spp. in subclinical mastitis in dairy herds in the state of Piauí,...
This research aimed to identify the diversity of bacterial species of the genus Staphylococcus spp. in subclinical mastitis in dairy herds in the state of Piauí, Northeastern Brazil, and to evaluate the phenotypic and genotypic resistance profile. Samples were obtained from a total of 17 dairy farms, amounting to 321 positive samples in the California Mastitis Test. Staphylococcus spp. were identified by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy. Subsequently, an antibiogram was performed, and a polymerase chain reaction was carried out to screen for resistance genes in the isolates. Among all the isolates, 59.45% (110/185) belonged to the Staphylococcus genus. Moreover, the following Staphylococcus spp. were identified Staphylococcus aureus, 68.1% (75/110); Staphylococcus chromogenes, 12.7% (14/110); Staphylococcus epidermidis, 5.4% (6/110); Staphylococcus sciuri, 4.5% (5/110); Staphylococcus warneri, 2.7% (3/110); Staphylococcus haemolyticus, 1.8% (2/110); Staphylococcus hominis, 1.8% (2/110); Staphylococcus arlettae, 0.9% (1/110); Staphylococcus capitis, 0.9% (1/110); and Staphylococcus gallinarum, 0.9% (1/110). The antibiogram showed a high frequency of resistance to penicillin and ampicillin, 70.0% (77/110) and 61.8% (68/110), respectively, and a low frequency of resistance to gentamicin and vancomycin, 10.9% (12/110) and 11.8% (13/110), respectively. In the genotypic tests for the different species of Staphylococcus spp., the occurrence of the blaZ gene was observed in 60.9% (67/110) of the isolates, followed by tetL and tetM, both with 20.0% (22/110) each, and the mecA and vanB genes were detected in 0.9% (1/110) of the samples. The identification of all Staphylococcus species isolated from subclinical mastitis cases and the phenotypic and genotypic resistance characterization in these isolates is of great importance for dairy farming in the state of Piauí, as well as for public health.
Topics: Cattle; Animals; Female; Humans; Mastitis, Bovine; Methicillin-Resistant Staphylococcus aureus; Brazil; Staphylococcus; Staphylococcal Infections; Microbial Sensitivity Tests; Milk; Anti-Bacterial Agents
PubMed: 36074251
DOI: 10.1007/s42770-022-00822-1 -
Antimicrobial Agents and Chemotherapy Dec 2017The novel 63,558-bp plasmid pSA-01, which harbors nine antibiotic resistance genes, including , (C), (L), (T), , , , , and (B), was characterized in strain SA-01,...
The novel 63,558-bp plasmid pSA-01, which harbors nine antibiotic resistance genes, including , (C), (L), (T), , , , , and (B), was characterized in strain SA-01, isolated from a chicken farm in China. The colocation of and genes was detected for the first time in an plasmid. The detection of two IS-mediated circular forms containing resistance genes in SA-01 suggested that IS may facilitate dissemination of antibiotic resistance genes.
Topics: Animals; Anti-Bacterial Agents; Bacterial Proteins; Chickens; China; Drug Resistance, Multiple, Bacterial; Farms; Fosfomycin; High-Throughput Nucleotide Sequencing; Microbial Sensitivity Tests; Plasmids; Poultry Diseases; Staphylococcal Infections; Staphylococcus
PubMed: 28923876
DOI: 10.1128/AAC.01388-17 -
Complete Genome Sequence of Staphylococcus arlettae AHKW2e, Isolated from a Dog's Paws in Hong Kong.Microbiology Resource Announcements Jul 2022Staphylococcus arlettae is commonly found on the skin of animals. Here, we describe the complete genome sequence of AHKW2e (2,649,260 bp; GC content, 33.6%), isolated...
Staphylococcus arlettae is commonly found on the skin of animals. Here, we describe the complete genome sequence of AHKW2e (2,649,260 bp; GC content, 33.6%), isolated from a dog's paws in Hong Kong, established through hybrid assembly and representing the second complete genome sequence of this species.
PubMed: 35758690
DOI: 10.1128/mra.00350-22 -
Frontiers in Microbiology 2018A substantial majority of global population owns cellular phones independently to demographic factors like age, economic status, and educational attainment. In this...
A substantial majority of global population owns cellular phones independently to demographic factors like age, economic status, and educational attainment. In this study, we investigated the diversity of microorganisms associated with cellular phones of 27 individuals using cultivation-based methods. Cellular phones were sampled using cotton swabs and a total of 554 isolates representing different morphotypes were obtained on four growth media. Matrix-assisted laser desorption ionization time of flight (MALDI-TOF) mass spectrometry could generate protein profiles for 527 isolates and species-level identification was obtained for 415 isolates. A dendrogram was constructed based on the protein profiles of the remaining isolates, to group 112 isolates under 39 different proteotypes. The representative strains of each group were selected for 16S rRNA gene and ITS region sequencing based identification. , , , and were the most frequently encountered bacteria, and , , , and were in case of fungi. At species-level the prevalence of , , , , , and was observed, most of these species are commensal microorganisms of human skin. UPGMA dendrogram and PCoA biplot generated based on the microbial communities associated with all cellular phones exhibited build-up of specific communities on cellular phones and the prevalence of objectionable microorganisms in some of the cellular phones can be attributed to the poor hygiene and sanitary practices. The study also revealed the impact of MALDI-TOF MS spectral quality on the identification results. Overall MALDI-TOF appears a powerful tool for routine microbial identification and de-replication of microorganisms. Quality filtering of MALDI-TOF MS spectrum, development of better sample processing methods and enriching the spectral database will improve the role of MALDI-TOF MS in microbial identifications.
PubMed: 29930546
DOI: 10.3389/fmicb.2018.01229 -
Microbiology Resource Announcements Nov 2019is one coagulase-negative species in the bacterial genus Here, we describe the closed complete genome sequence of strain P2, which was obtained using a hybrid...
is one coagulase-negative species in the bacterial genus Here, we describe the closed complete genome sequence of strain P2, which was obtained using a hybrid approach combining Oxford Nanopore long-read and Illumina MiSeq short-read sequencing data.
PubMed: 31699754
DOI: 10.1128/MRA.00696-19