High mortality associated with Catabacter hongkongensis bacteremia

Christensenella strain resources, genomic/metabolomic profiling, and association with host at species level

The gut commensal bacteria Christensenellaceae species are negatively associated with many metabolic diseases, and have been seen as promising next-generation probiotics. However, the cultured Christensenellaceae strain resources were limited, and their beneficial mechanisms for improving metabolic diseases have yet to be explored. In this study, we developed a method that enabled the enrichment and cultivation of Christensenellaceae strains from fecal samples. Using this method, a collection of Christensenellaceae Gut Microbial Biobank (ChrisGMB) was established, composed of 87 strains and genomes that represent 14 species of 8 genera. Seven species were first described and the cultured Christensenellaceae resources have been significantly expanded at species and strain levels. Christensenella strains exerted different abilities in utilization of various complex polysaccharides and other carbon sources, exhibited host-adaptation capabilities such as acid tolerance and bile tolerance, produced a wide range of volatile probiotic metabolites and secondary bile acids. Cohort analyses demonstrated that Christensenellaceae and Christensenella were prevalent in various cohorts and the abundances were significantly reduced in T2D and OB cohorts. At species level, Christensenellaceae showed different changes among healthy and disease cohorts. C. faecalis, F. tenuis, L. tenuis, and Guo. tenuis significantly reduced in all the metabolic disease cohorts. The relative abundances of C. minuta, C. hongkongensis and C. massiliensis showed no significant change in NAFLD and ACVD. and C. tenuis and C. acetigenes showed no significant change in ACVD, and Q. tenuis and Geh. tenuis showed no significant change in NAFLD, when compared with the HC cohort. So far as we know, this is the largest collection of cultured resource and first exploration of Christensenellaceae prevalences and abundances at species level.

Peritonitis with bacteremia due to Christensenella hongkongensis identified via ribosomal RNA sequencing in a Japanese patient with advanced colorectal adenocarcinoma: A case report

Background

Christensenella hongkongensis is an obligately anaerobic, catalase-positive, motile, non-sporulating, gram-positive coccobacillus. Human infections are rare and have not been previously reported in Japan. Herein, we report the first case of perforated peritonitis with C. hongkongensis bacteremia in Japan.

Case presentation

A 61-year-old Japanese man with advanced colorectal adenocarcinoma presented with fever and abdominal pain. Abdominal computed tomography revealed a low-density area with thinning of the sigmoid colon wall and air outside the intestinal tract, which was diagnosed as perforated peritonitis. Cultures of the ascitic fluid isolated Bacteroides fragilis, Bacteroides eggerthii, Parabacteroides distasonis, Enterococcus avium, and Candida albicans. Gram-positive rods were detected in the blood culture on admission after 4 days. The isolate was identified as C. hongkongensis via 16S ribosomal RNA (16S rRNA) sequencing. The patient underwent open abdominal washout and drainage via a transverse colon bifurcation colostomy. Intravenous meropenem (3 g/day) was administered for 5 days, followed by intravenous piperacillin-tazobactam (9 g/day) for 6 days, and then levofloxacin (500 mg/day) and metronidazole (1500 mg/day) intravenously for 15 days. Postoperatively, the patient gradually recovered. He was transferred to another palliative care hospital on day 38 after admission for worsening advanced colorectal cancer condition.

Conclusion

Bacteremia caused by C. hongkongensis is rare. 16S rRNA sequencing should be considered for the identification of gram-positive anaerobic rods that are difficult to diagnose by conventional methods.

Gut bacterial profiles in Parkinson's disease: A systematic review

INTRODUCTION

Recent advances have highlighted the relationships between gut dysbiosis and Parkinson's disease (PD). Microbiota transplantation from PD patients to mice can induce increased alpha-synuclein-mediated motor deficits. Human studies have identified differences in the gut microbiota of PD patients compared to healthy controls. We undertook a systematic review to evaluate the available evidence for the involvement of gut bacteria in the etiology of PD.

METHODS

The PubMed databank, the China National Knowledge Infrastructure databank, and Wanfang Data were searched from inception until June 2021 to identify human case-control studies that investigated relationships between PD and microbiota quantified from feces. We evaluated the resulting studies focusing on bacterial taxa that were different between PD patients and healthy controls.

RESULTS

Twenty-six studies were found in which 53 microbial families and 98 genera exhibited differences between patients with PD and healthy controls. The genera identified by more than two studies as increased in PD were Bifidobacterium, Alistipes, Christensenella, Enterococcus, Oscillospira, Bilophila, Desulfovibrio, Escherichia/Shigella, and Akkermansia, while Prevotella, Blautia, Faecalibacterium, Fusicatenibacter, and Haemophilus had three or more reports of being lower in PD patients. More than one report demonstrated that Bacteroides, Odoribacter, Parabacteroides, Butyricicoccus, Butyrivibrio, Clostridium, Coprococcus, Lachnospira, Lactobacillus, Megasphaera, Phascolarctobacterium, Roseburia, Ruminococcus, Streptococcus, and Klebsiella were altered in both directions.

CONCLUSION

Our review shows that the involvement of the gut microbiome in the etiology of PD may involve alterations of short-chain fatty acids (SCFAs)-producing bacteria and an increase in putative gut pathobionts. SCFAs-producing bacteria may vary above or below an "optimal range," causing imbalances. Considering that Bifidobacterium, Lactobacillus, and Akkermansia are beneficial for human health, increased Bifidobacterium and Lactobacillus in the PD gut microbiome may be associated with PD medications, especially COMT inhibitors, while a high level of Akkermansia may be associated with aging.

A fatal case associated with Catabacter hongkongensis bacteremia in lung cancer patient: A case report

Catabacter hongkongensis is a bacterium first isolated in 2007 and has since been detected in the blood of about fifteen patients with disease such as gastrointestinal malignancy, intestinal obstruction, or acute intestinal infection. We describe herein the case of a patient newly diagnosed with metastatic lung cancer, who died from a fatal infection possibly related to Catabacter hongkongensis bacteremia. By reviewing all cases reported in the literature, our case report supports that this infection is associated with a very high mortality in cancer patients.

Catabacter hongkongensis bacteremia identified by direct metagenomic sequencing of positive blood culture fluid, first case report in the US

Catabacter hongkongensis, an increasingly recognized bacteria in clinical samples, was identified by direct metagenomic sequencing of positive blood culture fluid from a 55-year-old patient with colonic perforation. The bacteremia was cleared by both antibiotic treatment and surgical intervention. This is the first case report of C. hongkongensis infection in the US.

Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis

The genera Catabacter (family 'Catabacteraceae') and Christensenella (family Christensenellaceae) are close relatives within the phylum Firmicutes. Members of these genera are strictly anaerobic, non-spore-forming and short straight rods with diverse phenotypes. Phylogenetic analysis of 16S rRNA genes suggest that Catabacter splits Christensenella into a polyphyletic clade. In an effort to ensure that family/genus names represent monophyletic clades, we performed a whole-genome based analysis of the genomes available for the cultured representatives of these genera: four species of Christensenella and two strains of Catabacter hongkongensis. A concatenated alignment of 135 shared protein sequences of single-copy core genes present in the included strains indicates that C. hongkongensis is indeed nested within the Christensenella clade. Based on their evolutionary relationship, we propose the transfer of Catabacter hongkongensis to the genus Christensenella as Christensenella hongkongensis comb. nov.

Phylogeny of Catabacter hongkongensis Strains Responsible for Bacteremia Is Not Associated with Clinical Outcomes or Therapeutic Efficacy

Catabacter hongkongensis is a Gram-positive rod, isolated in 2007 in blood culture. Fewer than 15 infections have been reported. Herein, we present a lethal case of bacteremia due to C. hongkongensis identified through phylogenetic analyses. A woman was found unconscious in a context of chronic diarrhea. An abdominal abscess with a hydroaeric level was discovered, associated with sigmoid adenocarcinoma and peritoneal carcinomatosis. Despite hospitalization in an ICU and the adaptation of antibiotic therapy, the patient died. Blood cultures were positive in the final stage of the disease (>60 h). Identification of C. hongkongensis was performed using 16S rDNA sequencing. Phylogenetic analyses did not enable classification of these strains according to clinical outcome or the antibiotic sensitivity to treatment. In this case, bacteria were difficult to isolate and MALDI-TOF remained non-contributive. As strains are resistant to probabilistic treatments, addition of metronidazole or vancomycin could optimize clinical management, highlighting the benefit of rapid molecular identification by sequencing.

The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health

The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date. The family is also related to a healthy status in a number of other different disease contexts, including obesity and inflammatory bowel disease. In addition, Christensenellaceae is highly heritable across multiple populations, although specific human genes underlying its heritability have so far been elusive. Further research into the microbial ecology and metabolism of these bacteria should reveal mechanistic underpinnings of their host-health associations and enable their development as therapeutics.

Streptococcus and Prevotella are associated with the prognosis of oesophageal squamous cell carcinoma

PURPOSE

Oesophageal squamous cell carcinoma (ESCC) is the dominant type of oesophageal cancer among the East Asian population. The role of ESCC tissue bacteria in neoplastic progression has not been fully elucidated. Our goal was to uncover different bacterial communities in pathological staging grouping of ESCC and to identify microorganisms that could predict the likelihood of prognosis.

METHODOLOGY

Tissue samples were obtained from 45 patients and assessed using 16S ribosomal RNA gene sequencing. Significant bacteria were selected to perform survival analysis and evaluate prognostic biomarker.Results/Key findings. We observed variations in the abundance of oesophageal flora among different pathological characteristics of ESCC. Phylum Bacteroidetes, Firmicutes and Spirochaetes showed significantly higher relative abundances among N+ (positive lymph node) patients when compared to N- (negative lymph node) controls, whereas Proteobacteria showed lower abundances in N+ patients. Both genera Prevotella and Treponema were more abundant in the N+ group. In regard to T stage, the abundance of only Streptococcus in T3-4 was significantly higher than that in T1-2, while the other genera showed no significance. On multivariable analysis adjusted for the effects of standard clinicopathological features, combined Streptococcus and Prevotella abundance retained its association with unfavourable survival (hazard ratio, 6.094; 95 % confidence interval, 1.072-34.646; P=0.042), suggesting that this may be an independent prognostic indicator for ESCC.

CONCLUSION

Combined Streptococcus and Prevotella abundance is regarded as an independent species prognostic biomarker in ESCC patients.

First case of human bacteraemia by Catabacter hongkongensis in Scandinavia

Catabacter hongkongensis was isolated and cultured from human blood for the first time in Scandinavia. The patient, an 83-year-old man from Dalarna, Sweden, recovered without antibiotic treatment, although a high mortality rate associated with C. hongkongensis infection had been reported from China, Canada and France. The genome of the strain ABBA15k was sequenced, assembled and analysed. In contrast to the type strain of the species HKU16^T, no antibiotic resistance was observed in Scandinavian strain ABBA15k. The strain was deposited as CCUG 68271, and the draft genome sequence is available from the DNA Data Bank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank under the accession number LLYX00000000.

First report of sepsis due to Catabacter hongkongensis in an Italian patient

The first isolation of Catabacter hongkongensis in Italy is reported. Pleomorphic Gram-positive rods were grown in blood cultures from samples obtained from a 55-year-old patient admitted to the intensive care unit with sepsis after he experienced massive thoracic and abdominal trauma. The identification was obtained by amplification and sequencing of the 16S rRNA gene.

First Report of Human Infection by Agromyces mediolanus, a Gram-Positive Organism Found in Soil

We report the first human infection by a member of the Agromyces genus, a group of Gram-positive bacteria found in soil. A patient with a long-term venous catheter developed bacteremia due to a non-vancomycin-susceptible isolate of Agromyces mediolanus. Rapid identification was possible by matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Draft Genome Sequence of Catabacter hongkongensis Type Strain HKU16T, Isolated from a Patient with Bacteremia and Intestinal Obstruction

We report the draft genome sequence of Catabacter hongkongensis, a catalase-positive bacterium which causes bacteremia with high mortality. The 3.2-Mb genome contains 3,161 protein coding sequences, including putative catalase and motility-related proteins, and antibiotic resistance genes, which could be important for its virulence and adaptation to diverse environments.

The first 1000 cultured species of the human gastrointestinal microbiota

The microorganisms that inhabit the human gastrointestinal tract comprise a complex ecosystem with functions that significantly contribute to our systemic metabolism and have an impact on health and disease. In line with its importance, the human gastrointestinal microbiota has been extensively studied. Despite the fact that a significant part of the intestinal microorganisms has not yet been cultured, presently over 1000 different microbial species that can reside in the human gastrointestinal tract have been identified. This review provides a systematic overview and detailed references of the total of 1057 intestinal species of Eukarya (92), Archaea (8) and Bacteria (957), based on the phylogenetic framework of their small subunit ribosomal RNA gene sequences. Moreover, it unifies knowledge about the prevalence, abundance, stability, physiology, genetics and the association with human health of these gastrointestinal microorganisms, which is currently scattered over a vast amount of literature published in the last 150 years. This detailed physiological and genetic information is expected to be instrumental in advancing our knowledge of the gastrointestinal microbiota. Moreover, it opens avenues for future comparative and functional metagenomic and other high-throughput approaches that need a systematic and physiological basis to have an impact.

List of new names and new combinations previously effectively, but not validly, published

The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

Amplicon pyrosequencing and ion torrent sequencing of wild duck eubacterial microbiome from fecal samples reveals numerous species linked to human and animal diseases

Our investigation into the composition of the wild duck,Aythya americana, eubacterial microbiome from a fecal sample using amplicon pyrosequencing revealed that the representative bacterial species were quite distinct from a pond water sample, and we were able to classify the major operational taxonomic units withFusobacterium mortiferum,Streptobacillus moniliformis,Lactobacillus intermedius,Actinomyces suimastitidis,Campylobacter Canadensis,Enterococcus cecorum,Lactobacillus aviarus,Actimomyces spp.,Pseudobutyrivibrio spp.and Helicobacter brantaerepresenting the majority of the eubacterial fecal microbiome.  Bacterial species present in the analysis revealed numerous organisms linked to human and animal diseases including septicemia, rat bite fever, pig mastitis, endocarditis, malar masses, genital infections, skin lesions, peritonitis, wound infections, septic arthritis, urocystitis, gastroenteritis and drinking water diseases.  In addition, to being known carriers of viral pathogens wild ducks should also be recognized as a potential source of a range of bacterial diseases.

Matrix-assisted laser desorption ionisation time-of-flight mass spectrometry for identification of clinically significant bacteria that are difficult to identify in clinical laboratories

AIMS

Although the revolutionary matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has been evaluated for identification of various groups of bacteria, its application in bacteria that are 'difficult-to-identify' by phenotypic tests has been less well studied. We aim to evaluate the usefulness of MALDI-TOF MS for identification of 'difficult-to-identify' bacterial isolates.

METHODS

We evaluated the performance of the Bruker MALDI-TOF MS system for a collection of 67 diverse clinically important bacterial isolates that were less commonly encountered, possessed ambiguous biochemical profiles or belonged to newly discovered species. The results were compared with 16S rRNA gene sequencing as a reference method for species identification.

RESULTS

Using 16S rRNA gene sequencing as the reference method, 30 (45%) isolates were identified correctly to species level (score ≥2.0), 20 (30%) were only identified to genus level (score ≥1.7), four (6%) were misidentified (incorrect species with score ≥2.0 or incorrect genus with score ≥1.7) and 13 (19%) showed 'no identification' (score <1.7). Aerobic Gram-positive bacteria showed the highest percentage of correct species identification, followed by aerobic Gram-negative, anaerobic Gram-positive and anaerobic Gram-negative bacteria. Sixteen isolates identified to genus level actually showed the correct species but with scores below the threshold for species identification. Most isolates which showed 'no identification' were due to the absence of the corresponding species in the Bruker database.

CONCLUSIONS

Expansion of commercial databases to include reference spectra of less commonly encountered and newly discovered species and to increase available spectra for each species is required to improve the accuracy of MALDI-TOF MS for identifying 'difficult-to-identify' bacteria.

Defining the vulnerable period for re-establishment of Clostridium difficile colonization after treatment of C. difficile infection with oral vancomycin or metronidazole

Background

Clostridium difficile is an anaerobic, spore-forming bacterium that is the most common cause of healthcare-associated diarrhea in developed countries. A significant proportion of patients receiving oral vancomycin or metronidazole for treatment of Clostridium difficile infection (CDI) develop recurrences. However, the period of vulnerability to re-establishment of colonization by C. difficile after therapy is not well defined.

Principal Findings

In a prospective study of CDI patients, we demonstrated that most vancomycin-treated patients maintained inhibitory concentrations of vancomycin in stool for 4 to 5 days after therapy, whereas metronidazole was only detectable during therapy. From the time of elimination of the antibiotics to 14 to 21 days after therapy, a majority of stool suspensions supported growth of C. difficile and deep 16S rRNA sequencing demonstrated persistent marked alteration of the indigenous microbiota. By 21 to 28 days after completion of CDI treatment, a majority of stool suspensions inhibited growth of C. difficile and there was evidence of some recovery of the microbiota.

Conclusions

These data demonstrate that there is a vulnerable period for re-establishment of C. difficile colonization after CDI treatment that begins within a few days after discontinuation of treatment and extends for about 3 weeks in most patients.