Whole-Genome Sequence of Staphylococcus hominis Strain J31 Isolated from Healthy Human Skin.
ABSTRACT: We report here the first whole-genome sequence of a skin-associated strain of Staphylococcus hominis determined using the PacBio long-read sequencing platform. S. hominis is a major commensal of the skin microflora. This genome sequence adds to our understanding of this species and will aid studies of gene traffic between staphylococci.
Project description:Staphylococcus hominis is frequently isolated from human skin, and we hypothesize that it may protect the cutaneous barrier from opportunistic pathogens. We determined that S. hominis makes six unique autoinducing peptide (AIP) signals that inhibit the major virulence factor accessory gene regulator (<i>agr</i>) quorum sensing system of Staphylococcus aureus. We solved and confirmed the structures of three novel AIP signals in conditioned medium by mass spectrometry and then validated synthetic AIP activity against all S. aureus <i>agr</i> classes. Synthetic AIPs also inhibited the conserved <i>agr</i> system in a related species, Staphylococcus epidermidis. We determined the distribution of S. hominis <i>agr</i> types on healthy human skin and found S. hominis <i>agr</i>-I and <i>agr</i>-II were highly represented across subjects. Further, synthetic AIP-II was protective <i>in vivo</i> against S. aureus-associated dermonecrotic or epicutaneous injury. Together, these findings demonstrate that a ubiquitous colonizer of human skin has a fundamentally protective role against opportunistic damage. <b>IMPORTANCE</b> Human skin is home to a variety of commensal bacteria, including many species of coagulase-negative staphylococci (CoNS). While it is well established that the microbiota as a whole maintains skin homeostasis and excludes pathogens (i.e., colonization resistance), relatively little is known about the unique contributions of individual CoNS species to these interactions. Staphylococcus hominis is the second most frequently isolated CoNS from healthy skin, and there is emerging evidence to suggest that it may play an important role in excluding pathogens, including Staphylococcus aureus, from colonizing or infecting the skin. Here, we identified that S. hominis makes 6 unique peptide inhibitors of the S. aureus global virulence factor regulation system (<i>agr</i>). Additionally, we found that one of these peptides can prevent topical or necrotic S. aureus skin injury in a mouse model. Our results demonstrate a specific and broadly protective role for this ubiquitous, yet underappreciated skin commensal.
Project description:We analyzed the occurrence and mechanisms of fusidic acid resistance present in staphylococci isolated from 59 healthy volunteers. The fingers of the volunteers were screened for the presence of staphylococci, and the collected isolates were tested for resistance to fusidic acid. A total of 34 fusidic acid resistant staphylococcal strains (all were coagulase-negative) were isolated from 22 individuals (22/59, 37.3%). Examination of the resistance genes revealed that acquired fusB or fusC was present in Staphylococcus epidermidis, Staphylococcus capitis subsp. urealyticus, Staphylococcus hominis subsp. hominis, Staphylococcus warneri and Staphylococcus haemolyticus. Resistance islands (RIs) carrying fusB were found in S. epidermidis and S. capitis subsp. urealyticus, while staphylococcal chromosome cassette (SCC)-related structures harboring fusC were found in S. hominis subsp. hominis. Genotypic analysis of S. epidermidis and S. hominis subsp. hominis indicated that the fus elements were disseminated in diverse genetic strain backgrounds. The fusC elements in S. hominis subsp. hominis strains were highly homologous to SCCfusC in the epidemic sequence type (ST) 239/SCCmecIII methicillin-resistant S. aureus (MRSA) or the pseudo SCCmec in ST779 MRSA. The presence of acquired fusidic acid resistance genes and their genetic environment in commensal staphylococci suggested that the skin commensal staphylococci may act as reservoir for fusidic acid resistance genes.
Project description:Staphylococcus hominis is a commensal resident of human skin and an opportunistic pathogen. The species is subdivided into two subspecies, S. hominis subsp. hominis and S. hominis subsp. novobiosepticus, which are difficult to distinguish. To investigate the evolution and epidemiology of S. hominis, a total of 108 isolates collected from 10 countries over 40 years were characterized by classical phenotypic methods and genetic methods. One nonsynonymous mutation in gyrB, scored with a novel SNP typing assay, had a perfect association with the novobiocin-resistant phenotype. A multilocus sequence typing (MLST) scheme was developed from six housekeeping gene fragments, and revealed relatively high levels of genetic diversity and a significant impact of recombination on S. hominis population structure. Among the 40 sequence types (STs) identified by MLST, three STs (ST2, ST16 and ST23) were S. hominis subsp. novobiosepticus, and they distinguished between isolates from different outbreaks, whereas 37 other STs were S. hominis subsp. hominis, one of which was widely disseminated (ST1). A modified PCR assay was developed to detect the presence of ccrAB4 from the SCCmec genetic element. S. hominis subsp. novobiosepticus isolates were oxacillin-resistant and carriers of specific components of SCCmec (mecA class A, ccrAB3, ccrAB4, ccrC), whereas S. hominis subsp. hominis included both oxacillin-sensitive and -resistant isolates and a more diverse array of SCCmec components. Surprisingly, phylogenetic analyses indicated that S. hominis subsp. novobiosepticus may be a polyphyletic and, hence, artificial taxon. In summary, these results revealed the genetic diversity of S. hominis, the identities of outbreak-causing clones, and the evolutionary relationships between subspecies and clones. The pathogenic lifestyle attributed to S. hominis subsp. novobiosepticus may have originated on more than one occasion.
Project description:<h4>Background</h4>Pentatrichomonas hominis inhabits the digestive tracts of several vertebrates, such as humans, monkeys, pigs, dogs, cats and rats. This protozoan was originally considered a commensal of the digestive tract but has subsequently been identified as a potential zoonotic parasite and a causative agent of diarrhoea. Molecular techniques are considered more sensitive and specific to detect P. hominis. This study aimed to determine the presence and genetic diversity of P. hominis in animals in Thailand. A total of 403 faecal samples were collected from 119 cats, 55 dogs, 73 goats, 35 monkeys, 55 cattle and 66 pigs, and the presence of P. hominis was determined using the nested polymerase chain reaction method. Sequence analysis of small-subunit ribosomal RNA genes was used to determine the genotype of the organism.<h4>Results</h4>Twenty-six samples (26/403, 6.45%) were positive for P. hominis. The highest prevalence was found in cats (21/119; 17.65%), followed by cattle (3/55; 5.45%) and dogs (2/55; 3.64%). Seven out of 26 nucleotides demonstrated 100% sequence identity with existing sequences; additionally, 16 novel sequence patterns were identified. All nucleotide sequences of P. hominis-positive samples were shown in the same branch with the previously described P. hominis sequences found in humans, dogs and goat.<h4>Conclusion</h4>This is the first study on P. hominis infections in animals in Thailand. Our findings revealed that the prevalence of P. hominis was significantly higher in cats than in cattle and dogs. Cats were the main reservoir host; however, P. hominis can infect several kinds of animals. Therefore, the proper waste management of animals is necessary to reduce and prevent infection in the community.
Project description:Impetigo is a contagious skin infection predominantly caused by <i>Staphylococcus aureus</i>. Decontamination of <i>S. aureus</i> from the skin is becoming more difficult because of the emergence of antibiotic-resistant strains. Bacteriophage endolysins are less likely to invoke resistance and can eliminate the target bacteria without disturbance of the normal microflora. In this study, we investigated the therapeutic potential of a recombinant endolysin derived from kayvirus S25-3 against staphylococcal impetigo in an experimental setting. First, the recombinant S25-3 endolysin required an incubation period of over 15 minutes to exhibit efficient bactericidal effects against <i>S. aureus</i>. Second, topical application of the recombinant S25-3 endolysin decreased the number of intraepidermal staphylococci and the size of pustules in an experimental mouse model of impetigo. Third, treatment with the recombinant S25-3 endolysin increased the diversity of the skin microbiota in the same mice. Finally, we revealed the genus-specific bacteriolytic effect of recombinant S25-3 endolysin against staphylococci, particularly <i>S. aureus</i>, among human skin commensal bacteria. Therefore, topical treatment with recombinant S25-3 endolysin can be a promising disease management procedure for staphylococcal impetigo by efficient bacteriolysis of <i>S. aureus</i> while improving the cutaneous bacterial microflora.
Project description:Cardiobacterium hominis is a well-known commensal bacterium of the oral cavity and an agent of infective endocarditis in humans. Here, we provide a draft genome sequence of a pathogenic strain isolated from blood cultures of a patient with infectious endocarditis.
Project description:Case series summary:Chronic diarrhea is a common and recurring problem in feline medicine. Intestinal trichomonads have been reported as causative agents of diarrhea in cats. While Pentatrichomonas hominis is considered commensal, Tritrichomonas foetus has been found to cause feline large bowel diarrhea in cats. In our report, two young cats infected with the feline leukemia virus (FeLV) and presenting with chronic diarrhea were identified as having trichomonads in their feces, based on direct examination and fecal culture. Molecular assays (PCR and DNA sequencing) revealed that the parasite involved was P hominis, not T foetus, as was suspected. The animals had already been subjected to ineffective therapy with metronidazole, and after the use of ronidazole, their feces became dry and formed. Relevance and novel information:This case report describes P hominis infection as a possible cause of chronic diarrhea in two young cats also infected by FeLV. The parasite was probably resistant to metronidazole, the drug of choice in the literature, and sensitive to ronidazole. Although considered commensal, P hominis infection should be evaluated as a differential diagnosis in cats with chronic diarrhea, especially those that are immunocompromised. Moreover, a combination of techniques such as direct examination and/or fecal culture and PCR is essential for an accurate diagnosis of P hominis infection.
Project description:Staphylococcus hominis is frequently isolated from human skin and we hypothesize that it may protect the cutaneous barrier from opportunistic pathogens. We determined that S. hominis makes six unique auto inducing peptide (AIP) signals that inhibit the major virulence factor accessory gene regulator (agr) quorum sensing system of Staphylococcus aureus. We solved and confirmed the structures of three novel AIP signals in conditioned media by mass spectrometry, then validated synthetic AIP activity against all S. aureus agr classes. Synthetic AIPs also inhibited the conserved agr system in a related species, Staphylococcus epidermidis. We determined the distribution of S. hominis agr types on healthy human skin and found S. hominis agr-I and agr-II were highly represented across subjects. Further, synthetic AIP-II was protective in vivo against S. aureus-associated dermonecrotic or epicutaneous injury. Together, these findings demonstrate that a ubiquitous colonizer of human skin has a fundamentally protective role against opportunistic damage. Overall design: We analyzed bacterial RNA from Staphylococcus hominis (strain C5) treated for 8 hours with DMSO (vehicle) or the AgrA inhibitor Apicidin (Parlet. Et al. Cell Rep. 2019) to determine genes under the transcriptional regulation of AgrA. Each group (treatment or control) contains three biological replicates for a total of 6 samples.
Project description:Investigation of changes in the skin microbiome following treatment of atopic dermatitis (AD) with dupilumab may provide valuable insights into the skin microbiome as a therapeutic target. The aim of this study is to assess changes in the AD skin microbiome following treatment of AD with dupilumab (<i>n</i> = 27). E-swabs were collected from nose, lesional, and nonlesional skin before and after 16 weeks of dupilumab therapy, and the microbiome was analyzed by 16S rRNA and <i>tuf</i> gene sequencing. Data for 17 patients with milder disease receiving treatment with non-targeted therapies are also presented. The results show that both groups experienced clinical improvement (<i>p</i> < 0.001) following dupilumab therapy and that Shannon diversity increased and bacterial community structure changed. The relative abundance of the genus <i>Staphylococcus</i> (S.) and <i>S. aureus</i> decreased, while that of S. <i>epidermidis</i> and <i>S. hominis</i> increased. No significant changes were observed for patients receiving non-targeted treatments. The increases in <i>S. epidermidis</i> and <i>S. hominis</i> and the decrease in <i>S. aureus</i> correlated with clinical improvement. Furthermore, changes in <i>S. hominis</i> and <i>S. epidermidis</i> correlated inversely with <i>S. aureus</i>. In conclusion, treatment with dupilumab significantly changed the skin microbiome and decreased <i>S. aureus</i>. Our results suggest a favorable role of commensal staphylococci in AD.
Project description:Pentatrichomonas hominis is considered a commensal protozoan in the large intestine of a number of mammalian hosts, such as cats, dogs, and non-human primates. The resulting infections, which can induce diarrhea, have been attributed to opportunistic overgrowth of P. hominis. This study was performed to confirm the P. hominis infection and its molecular characterization from the feces of puppies with diarrhea. Fecal samples were obtained from 14 German shepherd puppies with diarrhea over 1 week (7 females and 7 males, 2-9 months of age) residing on a dog farm in August 2007. Species-specific PCR assay identified P. hominis 18S rRNA genes in 3 of the 14 puppies (1 female and 2 males; 1 aged 2 months and 2 aged 9 months). This phylogenetic analysis established that P. hominis belonged to the 1st clade, which is comprised of Bos taurus and Felines.