Sphingobacterium spiritivorum infection in a patient with end stage renal disease on haemodialysis

Microbial landscapes of the rhizosphere soils and roots of Luffa cylindrica plant associated with Meloidogyne incognita

Introduction

The root-knot nematodes (RKN), especially Meloidogyne spp., are globally emerging harmful animals for many agricultural crops.

Methods

To explore microbial agents for biological control of these nematodes, the microbial communities of the rhizosphere soils and roots of sponge gourd (Luffa cylindrica) infected and non-infected by M. incognita nematodes, were investigated using culture-dependent and -independent methods.

Results

Thirty-two culturable bacterial and eight fungal species, along with 10,561 bacterial and 2,427 fungal operational taxonomic units (OTUs), were identified. Nine culturable bacterial species, 955 bacterial and 701 fungal OTUs were shared in both four groups. More culturable bacterial and fungal isolates were detected from the uninfected soils and roots than from the infected soils and roots (except no fungi detected from the uninfected roots), and among all samples, nine bacterial species (Arthrobacter sp., Bacillus sp., Burkholderia ambifaria, Enterobacteriaceae sp., Fictibacillus barbaricus, Microbacterium sp., Micrococcaceae sp., Rhizobiaceae sp., and Serratia sp.) were shared, with Arthrobacter sp. and Bacillus sp. being dominant. Pseudomonas nitroreducens was exclusively present in the infested soils, while Mammaliicoccus sciuri, Microbacterium azadirachtae, and Priestia sp., together with Mucor irregularis, Penicillium sp., P. commune, and Sordariomycetes sp. were found only in the uninfected soils. Cupriavidus metallidurans, Gordonia sp., Streptomyces viridobrunneus, and Terribacillus sp. were only in the uninfected roots while Aspergillus sp. only in infected roots. After M. incognita infestation, 319 bacterial OTUs (such as Chryseobacterium) and 171 fungal OTUs (such as Spizellomyces) were increased in rhizosphere soils, while 181 bacterial OTUs (such as Pasteuria) and 166 fungal OTUs (such as Exophiala) rose their abundance in plant roots. Meanwhile, much more decreased bacterial or fungal OTUs were identified from rhizosphere soils rather than from plant roots, exhibiting the protective effects of host plant on endophytes. Among the detected bacterial isolates, Streptomyces sp. TR27 was discovered to exhibit nematocidal activity, and B. amyloliquefaciens, Bacillus sp. P35, and M. azadirachtae to show repellent potentials for the second stage M. incognita juveniles, which can be used to develop RKN bio-control agents.

Discussion

These findings provided insights into the interactions among root-knot nematodes, host plants, and microorganisms, which will inspire explorations of novel nematicides.

An unusual cause of pyrexia of unknown origin with sepsis: A diagnostic challenge

Sphingobacterium species are ubiquitous and are abundant in nature and rarely involved in causing human infections. A 62-year-old man presented with recurrent episodes of high fever up to 40 ​°C accompanied by rigors, sweating, and malaise for the past 4 weeks. After a thorough workup, only elevated C-reactive protein with a leucocytosis was evident. Blood culture showed growth of Gram-negative bacilli which was identified as spingobacterium spiritivorum. Although S. spiritivorum is rare, with limited cases reported in the literature, it must be considered as a causative organism in patients with persistent fevers with sepsis.

Sphingobacterium Spritivorum Associated With Spontaneous Bacterial Peritonitis in a Cirrhotic Patient With Gram-Positive Bacteremia

Sphingobacterium spritivorum (SS) is a ubiquitous gram-negative organism and an uncommon cause of infection in humans. To our knowledge, there are no reported cases of this bacterium causing spontaneous bacterial peritonitis (SBP) in patients with cirrhosis. In this report, we discuss a case of a male patient in his late 60s who presented with severe sepsis from methicillin-resistant staphylococcus aureus (MRSA), in whom SS was subsequently identified via ascitic fluid culture. This unusual organism is known to have an innate resistance to multiple antibiotics and can cause life-threatening sepsis in cases of delayed or missed diagnosis. Clinicians should not be weighed down by anchoring bias and look for alternative, uncommon gram-negative organisms in cases of progressive sepsis in patients with ascites.

Scrub Typhus Complicated by Rare Human Pathogen Sphingobacterium spiritivorum

Sphingobacterium spiritivorum is a rare cause of human infections worldwide. After reviewing the literature, we could find only eight case reports to date. The majority of cases were of cellulitis and septicemia. Most of these patients were immunocompromised and the recovery rate was lesser. We present a case of a young female diagnosed with scrub typhus complicated by acute respiratory distress syndrome who developed septicemia and septic shock due to S. spiritivorum. She was managed with sensitive antibiotic levofloxacin, clinically improved, and discharged in satisfactory condition.

The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates

Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK^®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK^®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK^® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.

A rare case of endophthalmitis after bleb needle revision for glaucoma Xen® gel stent

PURPOSE

To describe the first case of endophthalmitis caused by Sphingobacterium spiritivorum, a glucose non-fermenting Gram-negative rod, in a patient previously implanted with a Xen^® gel stent.

CASE REPORT DESCRIPTION

An 83-year-old patient, affected by open-angle glaucoma and with a previous surgery of combined cataract extraction and Xen gel stent implantation, developed endophthalmitis 1 month after bleb needle revision with 5-fluorouracil injection. At presentation, best corrected visual acuity was hand movement, hypopyon was evident into the anterior chamber and a flat bleb with no sign of leakage was present over the Xen gel implant.

OUTCOME

Immediate pars plana vitrectomy was performed, with intravitreal antibiotic administration and silicon oil tamponade. S. spiritivorum was isolated from vitreous bacterial culture. According to the antibiogram, patient was treated with topical fortified ceftazidime eyedrops and appropriate systemic antibiotics (intravenous meropenem, 500 mg every 8 h for 7 days, followed by oral cotrimoxazole, 160 + 800 mg, twice a day for 10 days). After 2 weeks of treatment, ocular inflammation was resolved, best corrected visual acuity was 0.1 (Snellen chart) and intraocular pressure was 18 mm Hg without topical hypotensive therapy.

CONCLUSION

S. spiritivorum was isolated for the first time as a causative agent of endophthalmitis in humans. Bleb needle revision in patients with Xen gel implant is not free of complications, and an attentive follow-up is required.

Sphingobacterium spiritivorum bacteremia due to cellulitis in an elderly man with chronic obstructive pulmonary disease and congestive heart failure: a case report

Background

Sphingobacterium spiritivorum is a glucose non-fermenting Gram-negative rod, formerly classified as one of the Flavobacterium species. It is characterized by a large number of cellular membrane sphingophospholipids. Sphingobacterium species are ubiquitous and isolated from natural environments, such as soil and water. However, they rarely cause infections in humans. Only a limited number of cases have been reported in elderly and immunocompromised patients with underlying diseases and predisposing factors.

Case presentation

An 80-year-old Japanese man with chronic obstructive pulmonary disease and congestive heart failure visited the Kariya Toyota General Hospital, Aichi, Japan with the chief complaint of fever accompanied by chills and left leg pain. At initial presentation, he was distressed and dyspneic. He was febrile (38.8 °C), and his left foot was swollen with reddening and tenderness. We diagnosed him as having cellulitis, and he was hospitalized for antibiotic therapy. Initially, he was treated with intravenously administered cefazolin, but after the isolation of a glucose non-fermenting Gram-negative rod from blood cultures, we decided to switch cefazolin to intravenously administered meropenem on day 4, considering the antibiotic resistance of the causative organism. The causative organism was identified as S. spiritivorum on day 6. His condition gradually stabilized after admission. Meropenem was switched to orally administered levofloxacin on day 12. He was discharged on day 16 and treated successfully without any complications.

Conclusions

Although S. spiritivorum is rare, with limited cases isolated from cellulitis, it should be considered as a causative organism in elderly and immunocompromised patients with cellulitis. Blood cultures are the key to correct diagnosis and appropriate treatment.

Draft Genome Sequences of Two Strains of a Newly Described Species, Sphingobacterium cellulitidis

The draft genome sequences of two strains of a newly described species, Sphingobacterium cellulitidis, have been determined. The type strain originated from cellulitis of a toe of a patient and the other strain from the environment. The sequences will provide the reference genomes of the new Sphingobacterium species.

Bacterial communities in the small intestine respond differently to those in the caecum and colon in mice fed low- and high-fat diets

Bacterial communities in the mouse caecum and faeces are known to be altered by changes in dietary fat. The microbiota of the mouse small intestine, by contrast, has not been extensively profiled and it is unclear whether small intestinal bacterial communities shift with dietary fat levels. We compared the microbiota in the small intestine, caecum and colon in mice fed a low-fat (LF) or high-fat (HF) diet using 16S rRNA gene sequencing. The relative abundance of major phyla in the small intestine, Bacteriodetes, Firmicutes and Proteobacteria, was similar to that in the caecum and colon; the relative abundance of Verrucomicrobia was significantly reduced in the small intestine compared to the large intestine. Several genera were uniquely detected in the small intestine and included the aerotolerant anaerobe, Lactobacillus spp. The most abundant genera in the small intestine were accounted for by anaerobic bacteria and were identical to those identified in the large intestine. An HF diet was associated with significant weight gain and adiposity and with changes in the bacterial communities throughout the intestine, with changes in the small intestine differing from those in the caecum and colon. Prominent Gram-negative bacteria including genera of the phylum Bacteroidetes and a genus of Proteobacteria significantly changed in the large intestine. The mechanistic links between these changes and the development of obesity, perhaps involving metabolic endotoxemia, remain to be determined.

Molecular identification of bacterial endosymbionts of Sappinia strains

The genus Sappinia comprises free-living amoebae occurring worldwide in a variety of habitats such as soils, plant matter and freshwater ponds, but also animal faeces, and includes at present three species, S. pedata, S. diploidea and S. platani. The genus is potentially pathogenic, as indicated by the identification of S. pedata in a case of human amoebic encephalitis. Electron microscopy studies on some strains already revealed intracellular bacteria in Sappinia. In the current study, we performed 16S ribosomal RNA gene (rDNA) analysis of these bacterial endosymbionts. We first inferred relationships among Sappinia strains on the basis of 18S rDNA, demonstrating that S. pedata emerged as sister to a larger clade including S. diploidea, S. platani and a few 'S. diploidea-like' strains. Thus, bacterial 16S rDNA was searched for in representative strains of each Sappinia species/subgroup. We found that Sappinia strains were associated to distinct species of Flavobacterium or Pedobacter (phylum Bacteroidetes). These appear to be distributed following the amoebal host subgroups, and are not directly related to other Bacteroidetes species known as interacting with free-living amoebae. While all the endosymbionts' close relatives are known to grow on agar, bacteriological media inoculated with amoebal extracts remained negative. Overall, results indicate that the recovered bacteria are likely specific obligate endosymbionts of Sappinia species. Further studies, including additional amoebal strains and deep morphological and molecular analyses, will be necessary to confirm this hypothesis.