Erythema nodosum associated with Staphylococcus xylosus septicemia

Phenotypical characterization, and antibiotics susceptibility patterns of skin bacteria found in podoconiosis patients in the North West Region of Cameroon

BACKGROUND

Podoconiosis, a non-infectious disease originating from long-term exposure of bare feet to irritant red clay soil is a lifelong, disabling disease with no specific diagnostic tool, classified into 5 stages based on the severity of leg swelling (lymphoedema). Secondary bacterial infections have been suggested to cause acute dermatolymphangioadenitis (ADLA) attacks and drive disease progression. Although the North West Region of Cameroon has a proven history of podoconiosis endemicity, the bacterial composition of lymphoedema due to this condition has not been studied. Thus, this study investigated the leg bacterial diversity of patients who suffered from the lymphoedema and their susceptibility pattern to selected antibiotics.

METHODS

A cross-sectional study was carried out in which podoconiosis affected and non-lymphoedema individuals living in the same community were purposively selected. Samples were collected by swabbing the skin between the toes and around the anklebone, then cultured and sub-cultured on nutrient agar to obtain pure isolates. The cultured isolates were then morphologically and biochemically classified using microscopy and analytic profile index test kits, respectively. The disk diffusion technique was used to determine antibiotic susceptibility.

RESULTS

Thirty-three participants were recruited, and 249 bacterial isolates were characterized into 29 genera, 60 species; with 30 (50%) being gram positive rods, 19 (31.7%) gram positive cocci, and 11 (18.3%) gram negative rods. Thirteen gram positive rods, fifteen gram positive cocci, and eight gram negative rods of bacterial species were found only in podoconiosis individuals among which Cellulomonas spp / Microbacterium spp. (2.8%), Staphylococcus lentus (3.3%), and Burkholderia cepacia (4.0%) dominated. 90% (90%) of the bacterial isolates were sensitive to doxycycline, whereas ampicillin had a high level of intermediate resistance, and penicillin G had the greatest resistant profile.

CONCLUSION

Our findings show that 94 (37.8%) out of 249 described bacterial isolates were exclusively found in the legs of podoconiosis individuals, and their susceptibility pattern to antibiotics was similar to that of others.

Staphylococcal species composition in the skin microbiota of domestic pigeons (Columba livia domestica)

Staphylococci are a natural component of the skin microbiota of many organisms, including humans and birds. As opportunistic pathogens, they can cause a variety of infections in humans. The close contact between domestic pigeons and their owners provide an opportunity for exchange of skin-associated bacteria. In this study, 41 healthy racing pigeons were tested. Staphylococci were detected on the skin of each bird (41/41, 100%). Isolates were identified at the species level using matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). The diversity of the Staphylococcus species was relatively high and coagulase-negative staphylococci (CoNS) were predominantly isolated. In total, ten different staphylococcal species were identified. S. lentus (19/41, 46.3%) was noted most frequently. The pigeon skin was also inhabited by S. xylosus (6/41, 14.6%), S. equorum (4/41, 9.8%), S. hyicus (3/41, 7.3%), S. intermedius (2/41, 4.9%), S. sciuri (2/41, 4.9%), S. vitulinus (2/41, 4.9%), S. lugdunensis (1/41, 2.4%), S. hominis (1/41, 2.4%), and S. auricularis (1/41, 2.4%). Our results indicate that domestic pigeons may carry pathogens with zoonotic potential. All strains were susceptible to 12 antibiotics (ciprofloxacin, clindamycin chloramphenicol, erythromycin, fosfomycin, gentamicin, levofloxacin, norfloxacin, rifampicin, tobramycin, trimethoprim/sulfamethoxazole, vancomycin) representing 8 different classes. None isolate displayed a multidrug-resistant phenotype. Resistance to tetracycline (6/41, 14.6%) and to penicillin (4/41, 9.7%) was shown. The mecA gene was not detected in the examined strains and no methicillin-resistant staphylococci were found on the skin of the healthy pigeons.

Molecular Mechanism of Staphylococcus xylosus Resistance Against Tylosin and Florfenicol

Purpose

Drug resistance presents an ever-increasing global public health threat that involves all major microbial pathogens and antimicrobial drugs. Strains that are resistant to multiple drugs pose severe clinical problems and cost lives. However, systematic studies on cross-resistance of Staphylococcus xylosus have been missing.

Methods

Here, we investigated various mutations in the sequence of ribosomal proteins involved in cross-resistance. To understand this effect on a molecular basis and to further elucidate the role of cross-resistance, we computationally constructed the 3D model of the large ribosomal subunit from S. xylosus as well as its complexes with both tylosin and florfenicol. Meanwhile, all-atom molecular dynamics simulations was used. In addition, the regulation of protein networks also played an essential role in the development of cross-resistance in S. xylosus.

Results

We discovered that the minimum inhibitory concentration against both tylosin and florfenicol of the mutant strain containing the insertion L22 97KRTSAIN98 changed dramatically. Further, we found that unique structural changes in the β-hairpin of L22 played a central role in this variant in the development of antibiotic resistance in S. xylosus. The regulation of protein networks also played an essential role in the development of cross-resistance in S. xylosus.

Conclusion

Our work provides insightful views into the mechanism of S. xylosus resistance that could be useful for the development of the next generation of antibiotics.

Bacteriota and Antibiotic Resistance in Spiders

Simple Summary

The microbiomes of insects are known for having a great impact on their physiological properties for survival, such as nutrition, behavior, and health. In nature, spiders are one of the main insect predators, and their microbiomes have remained unclear yet. It is important to explore the microbiomes of spiders with the positive effect in the wild to gain an insight into the host–bacterial relationship. The insects have been the primary focus of microbiome studies from all arthropods. Although the research focused on the microbiome of spiders is still scarce, there is a possibility that spiders host diverse assemblages of bacteria, and some of them alter their physiology and behavior. According to our findings, there is a need for holistic microbiome studies across many organisms, which would increase our knowledge of the diversity and evolution of symbiotic relationships. Antimicrobial resistance is one of the most serious global public health threats in this century. Therefore, the knowledge and some information about insects and their ability to act as reservoirs of antibiotic-resistant microorganisms should be determined in order to ensure that they are not transferred to humans. It is important to monitor the microbiome of spiders found in human houses and the transmission of resistant microorganisms, which can be dangerous in relation to human health.

Abstract

Arthropods are reported to serve as vectors of transmission of pathogenic microorganisms to humans, animals, and the environment. The aims of our study were (i) to identify the external bacteriota of spiders inhabiting a chicken farm and slaughterhouse and (ii) to detect antimicrobial resistance of the isolates. In total, 102 spiders of 14 species were collected from a chicken farm, slaughterhouse, and buildings located in west Slovakia in 2017. Samples were diluted in peptone buffered water, and Tryptone Soya Agar (TSA), Triple Sugar Agar (TSI), Blood Agar (BA), and Anaerobic Agar (AA) were used for inoculation. A total of 28 genera and 56 microbial species were isolated from the samples. The most abundant species were Bacillus pumilus (28 isolates) and B. thuringensis (28 isolates). The least isolated species were Rhodotorula mucilaginosa (one isolate), Kocuria rhizophila (two isolates), Paenibacillus polymyxa (two isolates), and Staphylococcus equorum (two isolates). There were differences in microbial composition between the samples originating from the slaughterhouse, chicken farm, and buildings. The majority of the bacterial isolates resistant to antibiotics were isolated from the chicken farm. The isolation of potentially pathogenic bacteria such as Salmonella, Escherichia, and Salmonella spp., which possess multiple drug resistance, is of public health concern.

A Peek into the Bacterial Microbiome of the Eurasian Red Squirrel (Sciurus vulgaris)

Sciurus vulgaris (the Eurasian red squirrel) is native to Europe and Asia, but due to habitat destruction or fragmentation, interspecific competition, and infectious diseases, especially in European island areas the species finds itself at the brink of extinction. The repopulation of such bare habitats requires healthy squirrel specimens, either translocated from other wild habitats or reintroduced to the wilderness following captive breeding. Captivity, nonetheless, has shown an immense capacity to reshape the structure of wild species’ microbiota, adapting it to the less diverse diet and fewer environmental challenges. Therefore, assessing the differences between “wild” and “captive” microbiota in this species could elucidate if special living conditions are needed in order to augment the survival rate of specimens reintroduced into the wild. Furthermore, the microflora profile of the normal flora of healthy red squirrels raised in captivity could support clinicians in addressing infectious diseases episodes and also raise awareness on the zoonotic risk. Hence, this study aimed at documenting the bacterial species carried by S. vulgaris, disclosing overall similarities and variability patterns of the microbiota identified in individuals from two different living environments. We anticipated that the bacterial community would be less diverse in individuals raised in captivity, owing to their restrictive diet and to unchanging conditions in the enclosure. We also hypothesized that there would be a higher prevalence of zoonotic microorganisms in the captive animals, due to the proximity of humans and of other domestic species. To test this, samples (n = 100) were taken from five body regions of 20 red squirrels, both free-ranging and bred in captivity, processed by classical microbiology techniques, and further identified by biochemical assay (VITEK®2 Compact System). A relatively poor bacterial community, comprising 62 bacterial strains belonging to 18 species and 8 different genera, was identified. Most of these microorganisms were reported for the first time in S. vulgaris. With no discrimination between living environments, the highest prevalence (p < 0.001), was registered in Staphylococcus sciuri (60%; 12/20), followed by Escherichia coli (45%; 9/20) and Bacillus cereus (35%; 7/20). The results suggest unremarkable differences in diversity and richness of the resident aerobic microbiota of S. vulgaris, in relation to the living environment.

Rutin, A Natural Inhibitor of IGPD Protein, Partially Inhibits Biofilm Formation in Staphylococcus xylosus ATCC700404 in vitro and in vivo

Staphylococcus xylosus (S. xylosus) has become an emerging opportunistic pathogen due to its strong biofilm formation ability. Simultaneously, the biofilm of bacteria plays an important role in antibiotic resistance and chronic infection. Here, we confirmed that rutin can effectively inhibit biofilm formation in S. xylosus, of which the inhibition mechanism involves its ability to interact with imidazole glycerol phosphate dehydratase (IGPD), a key enzyme in the process of biofilm formation. We designed experiments to target IGPD and inhibited its activities against S. xylosus. Our results indicated that the activity of IGPD and the amount of histidine decreased significantly under the condition of 0.8 mg/ml rutin. Moreover, the expression of IGPD mRNA (hisB) and IGPD protein was significantly down-regulated. Meanwhile, the results from molecular dynamic simulation and Bio-layer interferometry (BLI) technique showed that rutin could bind to IGPD strongly. Additionally, in vivo studies demonstrated that rutin treatment reduced inflammation and protect mice from acute mastitis caused by S. xylosus. In summary, our findings provide new insights into the treatment of biofilm mediated persistent infections and chronic bacterial infections. It could be helpful to design next generation antibiotics to against resistant bacteria.

Nasal colonization and antibiotic resistance patterns of Staphylococcus species isolated from healthy horses in Tripoli, Libya

The present study investigated the colonization rates and antimicrobial susceptibility of Staphylococcus species isolated from the nostrils of healthy horses. A nonselective laboratory approach was applied, followed by confirmation using a Phoenix automated microbiological system. Among the 92 horses included in the study, 48.9% (45/92) carried Staphylococcus species of mostly the coagulase-negative staphylococci (CoNS) type yielding 70 Staphylococcus strains. Of these strains, 37.1% (26/70; 24 CoNS and 2 coagulase-positive staphylococci; CoPS) were identified as methicillin-resistant staphylococci (MRS) expressing significant resistance to important antimicrobial classes represented mainly by subspecies of CoNS. This is the first study reporting a high prevalence of various Staphylococcus species, particularly strains of CoNS expressing multidrug resistance patterns of public health concern, colonizing healthy horses in Libya.

Synanthropic spiders, including the global invasive noble false widow Steatoda nobilis, are reservoirs for medically important and antibiotic resistant bacteria

The false widow spider Steatoda nobilis is associated with bites which develop bacterial infections that are sometimes unresponsive to antibiotics. These could be secondary infections derived from opportunistic bacteria on the skin or infections directly vectored by the spider. In this study, we investigated whether it is plausible for S. nobilis and other synanthropic European spiders to vector bacteria during a bite, by seeking to identify bacteria with pathogenic potential on the spiders. 11 genera of bacteria were identified through 16S rRNA sequencing from the body surfaces and chelicerae of S. nobilis, and two native spiders: Amaurobius similis and Eratigena atrica. Out of 22 bacterial species isolated from S. nobilis, 12 were related to human pathogenicity among which Staphylococcus epidermidis, Kluyvera intermedia, Rothia mucilaginosa and Pseudomonas putida are recognized as class 2 pathogens. The isolates varied in their antibiotic susceptibility: Pseudomonas putida, Staphylococcus capitis and Staphylococcus edaphicus showed the highest extent of resistance, to three antibiotics in total. On the other hand, all bacteria recovered from S. nobilis were susceptible to ciprofloxacin. Our study demonstrates that S. nobilis does carry opportunistic pathogenic bacteria on its body surfaces and chelicerae. Therefore, some post-bite infections could be the result of vector-borne bacterial zoonoses that may be antibiotic resistant.

Erythema Nodosum Associated with Staphylococcus Species Infection in a Child

Erythema nodosum (EN) is a poly-etiological disease with an acute flow that is characterized by symmetric emergence of painful nodules often in pretibial areas.

A twenty-month-old male child was admitted to hospital for evaluation of the eruptive skin changes in the lower extremities and forearms. The disease began 10 days before getting febricity and loose stools. The laboratory analysis showed an elevated erythrocyte sedimentation rate and leukocytosis. Blood cultures demonstrated the presence of coagulase-negative Staphylococcus, while Proteus vulgaris was isolated in urine cultures. After initiation of the empiric antibiotic therapy and then, the targeted antibiotic therapy according to the antibiogram, there was a significant improvement in a general condition and regression of cutaneous lesions.

Erythema nodosum in the present case, is the result of staphylococcal bacteremia although Proteus vulgaris cannot be excluded as a cause.

Enterotoxigenicity and Antibiotic Resistance of Coagulase-Negative Staphylococci Isolated from Raw Buffalo and Cow Milk

Staphylococcal food poisoning is considered to be one of the most common foodborne illnesses worldwide. Because milk is rich in nutrients and its neutral pH, it leads to the growth of various bacteria. To date, the correlation between enterotoxigenic potential in Staphylococcus species and antimicrobial resistance (AMR), using bioinformatics analysis in buffalo and cow raw milk and the possible health risks from these bacteria, has not been examined in Egypt. A total of 42 Staphylococcus isolates representing 12 coagulase-positive staphylococci (Staphylococcus aureus and Staphylococcus intermedius) and 30 coagulase-negative staphylococci (Staphylococcus capitis, Staphylococcus xylosus, Staphylococcus carnosus, Staphylococcus saccharolyticus, and Staphylococcus auricularis) were isolated. An assay of the antimicrobial resistance phenotypes indicated low resistance against vancomycin (9.5%). The blaZ gene was associated with penicillin G and methicillin resistance and not with sulbactam + ampicillin. The presence of the gene ermB presented the correlation with erythromycin resistance and tetK with tetracycline resistance (correlation index: 0.57 and 0.49, respectively), despite the absence of the same behavior for ermC and tetM, respectively. Interestingly, the gene mecA was not correlated with resistance to methicillin or any other β-lactam. Correlation showed that slime-producing isolates had more resistance to antibiotics than those of nonslime producers. The multiple correlations between antibiotic resistance phenotypes and resistance genes indicate a complex nature of resistance in Staphylococcus species. The antimicrobial resistance could potentially spread to the community and thus, the resistance of Staphylococcus species to various antibiotics does not depend only on the use of a single antimicrobial, but also extends to other unrelated classes of antimicrobials.

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

Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources comprising stone fragments and sandy soil in James Ross Island, Antarctica. Here, we describe properties of a novel species of the genus Staphylococcus that has a 16S rRNA gene sequence nearly identical to that of Staphylococcus saprophyticus However, compared to S. saprophyticus and the next closest relatives, the new species demonstrates considerable phylogenetic distance at the whole-genome level, with an average nucleotide identity of <85% and inferred DNA-DNA hybridization of <30%. It forms a separate branch in the S. saprophyticus phylogenetic clade as confirmed by multilocus sequence analysis of six housekeeping genes, rpoB, hsp60, tuf, dnaJ, gap, and sod Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and key biochemical characteristics allowed these bacteria to be distinguished from their nearest phylogenetic neighbors. In contrast to S. saprophyticus subsp. saprophyticus, the novel strains are pyrrolidonyl arylamidase and β-glucuronidase positive and β-galactosidase negative, nitrate is reduced, and acid produced aerobically from d-mannose. Whole-genome sequencing of the 2.69-Mb large chromosome revealed the presence of a number of mobile genetic elements, including the 27-kb pseudo-staphylococcus cassette chromosome mec of strain P5085T (ψSCCmecP5085), harboring the mecC gene, two composite phage-inducible chromosomal islands probably essential to adaptation to extreme environments, and one complete and one defective prophage. Both strains are resistant to penicillin G, ampicillin, ceftazidime, methicillin, cefoxitin, and fosfomycin. We hypothesize that antibiotic resistance might represent an evolutionary advantage against beta-lactam producers, which are common in a polar environment. Based on these results, a novel species of the genus Staphylococcus is described and named Staphylococcus edaphicus sp. nov. The type strain is P5085T (= CCM 8730T = DSM 104441T).IMPORTANCE The description of Staphylococcus edaphicus 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 genomic characteristics presented here elucidate the evolutionary relationships in the Staphylococcus 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, S. edaphicus 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.

Francisella tularensis and other bacteria in hares and ticks in North Rhine-Westphalia (Germany)

Tularemia is a zoonotic disease caused by the bacterium Francisella tularensis. The disease can be transmitted to humans through contact with infected animals such as the European brown hare (Lepus europaeus) and ticks as vectors. The aim of this study was to isolate F. tularensis from ticks and hares in North Rhine-Westphalia using cysteine heart agar to determine their genetic relatedness and to identify other bacteria that grow on this medium. 848 European brown hares and 1556 questing ticks (all Ixodes ricinus) from forests were tested using cultivation and MALDI-TOF mass spectrometry or partial 16S rRNA gene sequencing. The majority of F. tularensis isolates from hares (n=24; 96%) and genomic F. tularensis DNA recovered from ticks belonged to the basal genetic clade IV and subclade B.18. These isolates were sensitive to erythromycin and were assigned to biovar I. Only a single strain isolated from a hare was assigned to basal clade I (B.12/B.35). All isolates were sensitive to tetracycline, doxycycline, streptomycin, gentamicin, chloramphenicol, and ciprofloxacin. Only 4 tick pools were positive for F. tularensis and cultivation was not successful in any of the pools. Most of the other isolated bacteria belonged to the order Bacillales with 36 Staphylococcus isolates, 9 Bacillus isolates and 8 Paenibacillus isolates. Prominent members of Enterobacterales were represented by different genera like Pantoea, Erwinia, Raoultella etc. Several of the bacterial species were soil or plant-associated, but some of the bacterial species were found in I. ricinus for the first time. Our results showed that F. tularensis was detected only in few ticks of an endemic area, but ticks were also infected by several other bacteria with zoonotic potential. Therefore, a wider spectrum of pathogens should be considered if a patient was bitten by a tick.

Rapid identification of staphylococci by Raman spectroscopy

Clinical treatment of the infections caused by various staphylococcal species differ depending on the actual cause of infection. Therefore, it is necessary to develop a fast and reliable method for identification of staphylococci. Raman spectroscopy is an optical method used in multiple scientific fields. Recent studies showed that the method has a potential for use in microbiological research, too. Our work here shows a possibility to identify staphylococci by Raman spectroscopy. We present a method that enables almost 100% successful identification of 16 of the clinically most important staphylococcal species directly from bacterial colonies grown on a Mueller-Hinton agar plate. We obtained characteristic Raman spectra of 277 staphylococcal strains belonging to 16 species from a 24-hour culture of each strain grown on the Mueller-Hinton agar plate using the Raman instrument. The results show that it is possible to distinguish among the tested species using Raman spectroscopy and therefore it has a great potential for use in routine clinical diagnostics.

The resident pathobiont Staphylococcus xylosus in Nfkbiz-deficient skin accelerates spontaneous skin inflammation

IκBζ, which is encoded by the Nfkbiz gene, is a member of the nuclear IκB family of proteins that act as transcriptional regulators via association with NF-κB. Nfkbiz-deficient (Nfkbiz ^-/-) mice develop spontaneous dermatitis; however, the underlying mechanism has yet to be elucidated. In our study, we found higher skin pathology scores and more serum IgE antibodies and trans-epidermal water loss in Nfkbiz ^-/- than in Nfkbiz-sufficient (Nfkbiz ^+/-) mice. There was also greater expansion of IFN-γ-, IL-17A-, and IL-22-secreting CD4⁺ T cells and of IL-17A-secreting γδ⁺ T cells in the skin of Nfkbiz ^-/- mice than in with Nfkbiz ^+/- mice. Pyrosequencing analysis showed decreased diversity of resident bacteria and markedly expanded Staphylococcus (S.) xylosus in the skin of Nfkbiz ^-/- mice. Oral administration of antibiotics including cephalexin and enrofloxacin ameliorated skin inflammation. Topical application of S. xylosus also resulted in the expansion of IL-17A-secreting CD4⁺ T cells along with high levels of pro-inflammatory cytokines and chemokines in the skin of Nfkbiz ^-/- mice. The expansion of commensal S. xylosus may be one cause of skin dysbiosis in Nfkbiz ^-/- mice and suggests that the Nfkbiz gene may play a regulatory role in the microbiota-skin immunity axis.

Genetic Diversity and Antibiotic Resistance Among Coagulase-Negative Staphylococci Recovered from Birds of Prey in Portugal

Wild animal populations in contact with antimicrobials and antimicrobial resistant bacteria that are daily released into the environment are able to become unintentional hosts of these resistant microorganisms. To clarify this issue, our study evaluated the presence of antibiotic resistance determinants on coagulase-negative staphylococci recovered from birds of prey and studied their genetic relatedness by pulsed-field gel electrophoresis (PFGE). The unusual vga(A) and erm(T) genes, which confer resistance to clindamycin and erythromycin, respectively, were detected in Staphylococcus sciuri or Staphylococcus xylosus strains and the tet(K) gene in Staphylococcus kloosii. The PFGE patterns showed that three S. xylosus (isolated of Strix aluco and Otus scops) and two S. sciuri (recovered from Strix aluco and Milvus migrans) were clonally indistinguishable. These animals could be a source of unusual antimicrobial resistance determinants for highly used antibiotics in veterinary clinical practice.

The novel macrolide-Lincosamide-Streptogramin B resistance gene erm(44) is associated with a prophage in Staphylococcus xylosus

A novel erythromycin ribosome methylase gene, erm(44), that confers resistance to macrolide, lincosamide, and streptogramin B (MLSB) antibiotics was identified by whole-genome sequencing of the chromosome of Staphylococcus xylosus isolated from bovine mastitis milk. The erm(44) gene is preceded by a regulatory sequence that encodes two leader peptides responsible for the inducible expression of the methylase gene, as demonstrated by cloning in Staphylococcus aureus. The erm(44) gene is located on a 53-kb putative prophage designated ΦJW4341-pro. The 56 predicted open reading frames of ΦJW4341-pro are structurally organized into the five functional modules found in members of the family Siphoviridae. ΦJW4341-pro is site-specifically integrated into the S. xylosus chromosome, where it is flanked by two perfect 19-bp direct repeats, and exhibits the ability to circularize. The presence of erm(44) in three additional S. xylosus strains suggests that this putative prophage has the potential to disseminate MLSB resistance.