Cellulitis and bacteremia caused by Bergeyella zoohelcum

Characterization and the first complete genome sequence of a novel strain of Bergeyella porcorum isolated from pigs in China

BACKGROUND

Bergeyella porcorum is a newly identified bacterium that has an ambiguous relationship with pneumonia in pigs. However, few studies have adequately characterized this species.

RESULTS

In this study, we analyzed the morphological, physiological, and genomic characteristics of the newly identified B. porcorum sp. nov. strain QD2021 isolated from pigs. The complete genome sequence of the B. porcorum QD2021 strain consists of a single circular chromosome (2,271,736 bp, 38.51% G + C content), which encodes 2,578 genes. One plasmid with a size of 70,040 bp was detected. A total of 121 scattered repeat sequences, 319 tandem repeat sequences, 4 genomic islands, 5 prophages, 3 CRISPR sequences, and 51 ncRNAs were predicted. The coding genes of the B. porcorum genome were successfully annotated across eight databases (NR, GO, KEGG, COG, TCDB, Pfam, Swiss-Prot and CAZy) and four pathogenicity-related databases (PHI, CARD, VFDB and ARDB). In addition, a comparative genome analysis was performed to explore the evolutionary relationships of B. porcorum QD2021.

CONCLUSIONS

To our knowledge, this is the first study to provide fundamental phenotypic and whole-genome sequences for B. porcorum. Our results extensively expand the current knowledge and could serve as a valuable genomic resource for future research on B. porcorum.

Copper exposure causes alteration in the intestinal microbiota and metabolites in Takifugu rubripes

Copper is an environmental pollutant, and copper in aquatic environments mainly comes from soil and water. It enters the environment through atmospheric deposition, sewage discharge, and industrial production, and enters aquatic organisms, causing toxicity. Takifugu rubripes (T. rubripes) is a marine fish with high economic value. Due to the toxic effects of heavy metals on aquatic organisms such as fish, it can affect the gut community and metabolites of fish. The gut is an important channel for fish to communicate with the outside world and a necessary pathway for the metabolism of nutrients and toxic substances in the fish body. Studies have shown that due to changes in global water emissions and the high sensitivity of aquatic organisms to the environment, copper may pose greater potential hazards to aquatic organisms. Copper poses a greater risk to aquatic species than other heavy metals and metal/metal like pollutants (such as cadmium, lead, mercury, arsenic, etc.) . In order to elucidate the effects of copper exposure on the gut of T. rubripes. In this study, we exposed T. rubripes to 0, 50, 100, or 500 μg/L of copper for three days, the effects of copper exposure on the gut microbiota structure and metabolites of the T. rubripes were investigated using 16 S rRNA gene and metabolomics techniques. The research results indicate that with the increase copper concentration, the intestinal tissue of T. rubripes undergoes significant damage. 16 S rRNA sequencing results show that copper exposure alters the structure and metabolites of intestinal microbiota. Copper exposure of 100 and 500 μg/L inhibited the colonization of the bacterial gut, disrupted the intestinal barrier, and made the fish susceptible to the pathogens. Liquid chromatography-mass spectrometry analysis showed that copper regulated the production of metabolites such as L-histidine, arachidonic acid, and L-glutamic acid, which are related to energy and immunity. Microbiome-metabolome correlation analysis showed that Subdoligranulum, Family_XIII_AD3011_group, and Clostridium_sensu_stricto_1 were the key bacteria for copper ion intervention, and they might up-regulate the levels of metabolites such as indole-3-acetic acid, 3-indoleacrylic acid, and 5-hydroxyindole in the tryptophan metabolism pathway. In summary, our research has demonstrated that copper exposure can cause pathological changes in the intestinal tissue of the T. rubripes. High concentrations of copper ions can affect the colonization of the T. rubripes microbiota in the intestine, damage the fish's immune system, and alter the structure and metabolites of the intestinal microbiota, this can lead to intestinal metabolic dysfunction. providing a reference for the evaluation of the biological toxicity effects of heavy metal elements in the marine environment. This study provides a reference for evaluating the biological toxicity effects of heavy metal elements in marine environments.

The Identification of Multidrug-Resistant Microorganisms including Bergeyella zoohelcum Acquired from the Skin/Prosthetic Interface of Amputees and Their Susceptibility to Medihoney™ and Garlic Extract (Allicin)

Users of prosthetic devices face the accumulation of potentially drug-resistant pathogenic bacteria on the skin/prosthesis interface. In this study, we took surface swabs of the skin/prosthesis interface of eleven disabled athletes to identify microorganisms present. In addition to determining their antimicrobial resistance profile, we assessed their sensitivity to Manuka honey and Garlic extract (allicin). Eleven volunteers were directed to swab the skin at the skin/prosthesis interface. After initial isolation of microorganisms, we employed the following general microbiological methods: Gram stain, Catalase test, Oxidase test, lactose fermenting capability, haemolytic capability, Staphaurex, mannitol fermenting capability, Streptex; API Staph, 20E, Candida, and BBL crystal identification system tests. Once identified, isolates were analysed for their sensitivity to penicillin, erythromycin, ampicillin, vancomycin, ceftazidime, ciprofloxacin, gentamicin, and colistin-sulphate. Isolates were also analysed for their sensitivity to allicin (Garlic Extract (GE)) and Manuka honey (Medihoney™) (MH). Eleven isolates were identified: Bacillus cereus, Staphylococcus haemolyticus, Staphylococcus aureus, Micrococcus luteus, Pseudomonas oryzihabitans, Micrococcus spp., Bacillus subtilis, Group D Streptococcus, Pantoea spp., Enterobacter cloacae, and Bergeyella zoohelcum. All isolates were resistant to 1 unit of penicillin and 10 μg of ampicillin. Bergeyella zoohelcum was observed to have the widest range of resistance with observed resistance against five of the eight antimicrobials employed in this study. This study highlights the prevalence of uncommon drug-resistant microorganisms on the skin within a vulnerable population, highlighting the potential for MH or GE intervention.

Colorectal Tumour Mucosa Microbiome Is Enriched in Oral Pathogens and Defines Three Subtypes That Correlate with Markers of Tumour Progression

Long-term dysbiosis of the gut microbiome has a significant impact on colorectal cancer (CRC) progression and explains part of the observed heterogeneity of the disease. Even though the shifts in gut microbiome in the normal-adenoma-carcinoma sequence were described, the landscape of the microbiome within CRC and its associations with clinical variables remain under-explored. We performed 16S rRNA gene sequencing of paired tumour tissue, adjacent visually normal mucosa and stool swabs of 178 patients with stage 0-IV CRC to describe the tumour microbiome and its association with clinical variables. We identified new genera associated either with CRC tumour mucosa or CRC in general. The tumour mucosa was dominated by genera belonging to oral pathogens. Based on the tumour microbiome, we stratified CRC patients into three subtypes, significantly associated with prognostic factors such as tumour grade, sidedness and TNM staging, BRAF mutation and MSI status. We found that the CRC microbiome is strongly correlated with the grade, location and stage, but these associations are dependent on the microbial environment. Our study opens new research avenues in the microbiome CRC biomarker detection of disease progression while identifying its limitations, suggesting the need for combining several sampling sites (e.g., stool and tumour swabs).

Characterization and whole genome sequencing of a novel strain of Bergeyella cardium related to infective endocarditis

Background

Bergeyella cardium infection is becoming increasingly prevalent in patients with infective endocarditis, suggesting its significance in disease pathogenesis. However, few studies have fully characterized this species.

Results

Herein, we report the morphological and physiological characteristics, as well as whole genome sequencing of a newly identified B. cardium HPQL strain isolated from a patient with infective endocarditis. Results from the cellular morphology and biochemical analysis provide basic knowledge on the new pathogen. The whole genome sequencing of B. cardium HPQL consists of a circular chromosome with a total length of 2,036,890 bp. No plasmid was detected. Comparative genomics were carried out then. Antibiotics resistance related genes, pathogenesis related genes, predicted insertion sequences, genome islands and predicted CRISPRs sequences were demonstrated. To our knowledge, this is the first study to provide a complete genome sequence for Bergeyella spp.

Conclusions

This study provides fundamental phenotypic and genomic information for the newly identified fastidious infective endocarditis causative bacteria, B. cardium. Our results provide insights into effective clinical diagnosis and treatment of this pathogen.

Bergeyella zoohelcum isolated from oral cavities of therapy dogs

Bergeyella zoohelcum causes rare but severe human clinical diseases, which mostly arise from animal bites. Notably, Bergeyella infections can also occur in older people after prolonged exposure to dogs or cats without biting. We detected B. zoohelcum in oral cavities of therapy dogs in close contact with older people residing in nursing homes. Twenty-two bacterial isolates were identified as B. zoohelcum by using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing. Our results showed that MALDI-TOF MS is an effective tool for rapid identification of rarely isolated, difficult-to-identify microorganisms, such as B. zoohelcum, derived from not only human clinical samples but also animal samples. To our knowledge, this is the first report on detection of B. zoohelcum from therapy dogs. We have provided information on dog-assisted therapy to improve the relationship between humans and animals in ageing societies, particularly for preventive healthcare of older people living in nursing care facilities.

Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats

The taxonomy of marine and non-marine organisms rarely overlap, but the mechanisms underlying this distinction are often unknown. Here, we predicted three major ocean-to-land transitions in the evolutionary history of Flavobacteriaceae, a family known for polysaccharide and peptide degradation. These unidirectional transitions were associated with repeated losses of marine signature genes and repeated gains of non-marine adaptive genes. This included various Na⁺ -dependent transporters, osmolyte transporters and glycoside hydrolases (GH) for sulfated polysaccharide utilization in marine descendants, and in non-marine descendants genes for utilizing the land plant material pectin and genes facilitating terrestrial host interactions. The K⁺ scavenging ATPase was repeatedly gained whereas the corresponding low-affinity transporter repeatedly lost upon transitions, reflecting K⁺ ions are less available to non-marine bacteria. Strikingly, the central metabolism Na⁺ -translocating NADH: quinone dehydrogenase gene was repeatedly gained in marine descendants, whereas the H⁺ -translocating counterpart was repeatedly gained in non-marine lineages. Furthermore, GH genes were depleted in isolates colonizing animal hosts but abundant in bacteria inhabiting other non-marine niches; thus relative abundances of GH versus peptidase genes among Flavobacteriaceae lineages were inconsistent with the marine versus non-marine dichotomy. We suggest that phylogenomic analyses can cast novel light on mechanisms explaining the distribution and ecology of key microbiome components.

Bacteremia caused by Bergeyella zoohelcum in an infective endocarditis patient: case report and review of literature

Background

Bergeyella zoohelcum is an aerobic, Gram-negative bacterium that is frequently isolated from the upper respiratory tract of dogs, cats and other mammals. Clinically, B. zoohelcum has been reported causing cellulitis, tenosynovitis, leg abscess and septicemia, which is closely connected with animal bites. Here we describe a case of bacteremia in an infective endocarditis (IE) patient caused by B. zoohelcum, in China.

Case presentation

A 27-year-old infective endocarditis woman who had no history of dog bite nor other mammal exposure suffered bacteremia caused by B. zoohelcum. This patient, without evidence of polymicrobial infection, was treated with cefuroxime and had a good outcome.

Conclusions

B. zoolhelcum bacteremia is rarely reported in IE patients. Our report expands the range of known bacterial causes of infective endocarditis.

Bergeyella porcorum sp. nov., isolated from pigs

Four Gram-stain-negative, catalase- and oxidase-positive, bacillus-shaped bacterial isolates were recovered from the lungs and tonsils of four pigs. Based on cellular morphology and biochemical criteria the isolates were tentatively assigned to the genus Bergeyella, although the organisms did not appear to correspond with Bergeyella zoohelcum, the only validly named species of this genus. 16S rRNA gene sequencing demonstrated that isolates represented a distinct subline within the genus Bergeyella with <97%. 16S rRNA gene sequence similarity with B. zoohelcum ATCC 43767(T). The predominant cellular fatty acids of strain 1350-03(T) were iso-C15:0 and iso-C17:0 3-OH and the major quinone was MK-6. The DNA G+C content of strain 1350-03(T) was 37.7mol%. The novel isolates can be phenotypically distinguished from B. zoohelcum based on physiological traits. On the basis of both phenotypic and phylogenetic findings, we describe a new species of the genus Bergeyella for which we propose the name of Bergeyella porcorum sp. nov. (1350-03(T)=CCUG 67887(T)=CECT 9006(T)).

Bergeyella zoohelcum Associated with Abscess and Cellulitis After a Dog Bite

Cat and dog bites are a common cause of injury in young children. Bergeyella zoohelcum is a rarely reported zoonotic pathogen that is a part of cat and dog oral flora. We present a case of a child with B. zoohelcum abscess and cellulitis after a dog bite and review previously reported cases.

A new causative bacteria of infective endocarditis, Bergeyella cardium sp. nov

The first cases of infective endocarditis due to a new species of Bergeyella, Bergeyella cardium sp. nov., are reported. Two strains, 13-07(T) (= JCM 30115(T) = NCCP 15908(T)) and 13-16, were independently isolated from 2 patients in different hospitals in Korea. Initially, the isolates were identified as Brevundimonas spp.; however, their 16S rRNA gene sequences shared a similarity of 94.9% with Bergeyella zoohelcum, implying that they are a new species belonging to of the genus Bergeyella. The organisms might be susceptible to many commonly used antibiotics, including penicillin. The first case was successfully treated with ceftriaxone, and the second, with piperacillin/tazobactam plus amikacin.