Dysgonomonas capnocytophagoides bacteraemia in a neutropenic patient treated for acute myeloid leukaemia

Dysgonomonas mossii Strain Shenzhen WH 0221, a New Member of the Genus Dysgonomonas Isolated from the Blood of a Patient with Diabetic Nephropathy, Exhibits Multiple Antibiotic Resistance

Herein, we present a new bacterial strain isolated from infected blood of a patient with diabetic nephropathy. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry failed to identify the strain. 16S rRNA gene sequencing showed the highest similarity (>99.5%) with genus Dysgonomonas, but the strain could not be distinguished from Dysgonomonas oryzarvi and Dysgonomonas mossii. Whole genome sequencing, followed by phylogenetic analysis and average nucleotide identity (>95%) analysis, confirmed that the new strain represented Dysgonomonas mossii, leading it to be named Dysgonomonas mossii strain Shenzhen WH 0221. Shenzhen WH 0221 was 3.60 Mb with 37.4% GC content. It was Gram-stain negative, facultatively anaerobic, and grown on Columbia agar supplemented with 5% of sheep blood, exhibiting a smooth surface and pinpoint morphology. The morphological characteristics of this strain include a short rod shape without flagella and a size of 0.45-0.55 × 0.95-1.52 μm observed under transmission electron microscopy. The physiological and biochemical features and major cellular fatty acids (characterized by C_14:0 3-OH, C_14:0 9-CH₃, and C_16:0) differed from D. mossii CCUG 43457^T and other members of the genus Dysgonomonas. The isolate was found resistant to most cephalosporins, penicillin, norfloxacin, vancomycin, and chloramphenicol, but was susceptible to meropenem, imipenem, tetracycline, clindamycin, and amoxicillin-clavulanic acid. Genes kdpE, ykkD, cmeB, TLA-3, and vanRM found in its genome are probably associated with multiple antibiotic resistance. Lipopolysaccharides, capsules, and cytolysin may also help to illuminate its potential pathogenicity. This is the first report of a case of sepsis caused by Dysgonomonas mossii, and its pathogenic system was analyzed by whole genome sequencing. IMPORTANCE This study identified a new strain, Dysgonomonas mossii strain Shenzhen WH 0221, which has been first reported to cause sepsis isolated from infected blood of a patient with diabetic nephropathy. Physiological and biochemical characterizations, as well as overall fatty acid profile, distinguish Shenzhen WH 0221 from other species of the same genus. However, limited antibiotics were researched for Dysgonomonas mossii. Seventeen antibiotics spanning at least 6 classes were studied, providing a valuable guide to the clinical usage of drugs to treat Dysgonomonas mossii infection. For the first time, we report genome-based functional predictions for Dysgonomonas mossii. Five antibiotic resistance ontologies and more than 200 virulence factors likely underlie the multidrug resistance of Shenzhen WH 0221 and its potential pathogenicity.

Dysgonomonas capnocytophagoides Bacteremia in a Patient With Stage IV Colon Adenocarcinoma

Dysgonomonas capnocytophagoides bacteremia is a rare clinical entity described in only five case reports. Difficulties in the identification and intrinsic multidrug resistance (MDR) of the organism make diagnosis and treatment challenging. We present a case of D. capnocytophagoides bacteremia which highlights the diagnostic and treatment challenges posed by this organism. The case also contributes to the nascent understanding of the clinical profile of patients with D. capnocytophagoides infection and the antimicrobial susceptibility of the organism. A 56-year-old male with advanced colon adenocarcinoma on palliative fluorouracil, leucovorin, and irinotecan (FOLFIRI) presented with abdominal pain. He had been discharged recently following an ICU admission for neutropenic fever with diarrhea and polymicrobial bacteremia resulting in sepsis. Diarrhea resolved during hospitalization. Mediport was retained, surveillance blood cultures remained negative, and he completed 14 days of levofloxacin. Upon readmission for abdominal pain, vital signs were normal and neutropenia had resolved. A Gram-negative rod grew from blood cultures drawn peripherally and from the port with no differential time-to-positivity. Multiple testing platforms were used in an attempt to identify the organism, to include the VERIGENE® Gram-negative blood culture test, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, VITEK ® 2 GN ID, and the Thermo Scientific™ RapID™ NH System (Thermo Scientific, Waltham, MA). Test results from all platforms were either inconclusive or contradictory in their identification of the organism, making the determination of appropriate treatment difficult. Given inconsistent results on multiple testing platforms, the isolate was sent for whole genome sequencing (WGS). Additional workup performed during the hospitalization included a diagnostic paracentesis without evidence of spontaneous bacterial peritonitis, transesophageal echocardiogram without evidence of infective endocarditis, and dental evaluation without evidence of the infectious source. Abdominal CT showed nonspecific terminal ileitis. He was treated for presumed HACEK bacteremia and was transitioned from piperacillin-tazobactam to ceftriaxone to complete a two-week course at hospital discharge. He also received a seven-day course of doxycycline for concomitant, mild lower extremity cellulitis which resolved during hospitalization. Ultimately, antimicrobial susceptibility testing which resulted following discharge was not consistent with the HACEK organism. Testing demonstrated resistance to multiple antimicrobials including ceftriaxone, as well as susceptibility to trimethoprim-sulfamethoxazole (TMP/SMX). WGS ultimately identified the organism as D. capnocytophagoides. Despite ceftriaxone resistance, he reported feeling well at follow-up with negative surveillance blood cultures. This patient shares several features with the few patients previously identified with D. capnocytophagoides bacteremia, including malignancy, recent neutropenia, and presumed gastrointestinal source. As in the small number of prior reported cases, the organism was difficult to identify leading to delay in diagnosis and treatment. The case demonstrates the importance of critical thinking in the face of contradictory test results. Additionally, based on susceptibility profiles described in prior literature, we suspect doxycycline treated his bacteremia.

Exogenous and endogenous microbiomes of wild-caught Phormia regina (Diptera: Calliphoridae) flies from a suburban farm by 16S rRNA gene sequencing

The black blow fly, Phormia regina (Meigen) (Diptera: Calliphoridae) is one of the most abundant carrion flies in North America. Calliphorids are important in agriculture and animal production, veterinary sciences, forensics and medical entomology. While the role of flies in the epidemiology of human and animal diseases is an active area of research, little is known about the microorganisms associated with these insects. We examined the diversity of wild-caught black blow fly endogenous (internal body) and exogenous (external body) microbial communities using 16S rRNA gene sequencing. Overall, 27 phyla, 171 families and 533 genera were detected, and diversity was significantly higher (P < 0.05) on external body surfaces. At the genus level, Dysgonomonas, Ignatzschineria, Acinetobacter, Vagococcus, Myroides, and Wohlfahrtiimonas were predominant. Cloning and sequencing of nearly full-length fragments of the 16S rRNA gene showed that some of the species identified are known to be pathogenic to humans, animals, and plants. Myroides odoratimimus and Acinetobacter radioresistens are well-known, multi-drug resistant bacteria. These results provide a snapshot of the microbial communities harbored by adult black blow flies and call for more comprehensive studies to better characterize the role these flies may play in the transmission of pathogenic microorganisms.

First case report of bacteremia caused by Dysgonomonas mossii

We here report a case of Dysgonomonas mossii bacteremia with cholangitis. An 85-year-old male patient with recurrent hepatitis B surface antigen-negative/anti-hepatitis C virus-negative hepatocellular carcinoma came to our hospital in poor physical condition. Two sets of blood cultures revealed a positive result for D. mossii. As matrix-assisted laser desorption/ionization time-of-flight mass spectrometry failed to identify D. mossii, analysis of 16S rRNA gene sequencing was performed; however, this gene is not specific enough to distinguish between D. mossii and D. oryzarvi. Finally, D. mossii infection was confirmed by gyrB and recA sequencing. To our knowledge, this is the first report of D. mossii causing human infection, which was identified in culture and confirmed using a combination of 16S rRNA, gyrB, and recA sequencing.

Ginsenosides Rb3 and Rd reduce polyps formation while reinstate the dysbiotic gut microbiota and the intestinal microenvironment in ApcMin/+ mice

Studies showed that manipulation of gut microbiota (GM) composition through the treatment of prebiotics could be a novel preventive measure against colorectal cancer (CRC) development. In this study, for the first time, we assessed the non-toxic doses of the triterpene saponins (ginsenoside-Rb3 and ginsenoside-Rd) - as prebiotics - that effectively reinstated the dysbiotic-gut microbial composition and intestinal microenvironment in an Apc^Min/+ mice model. Rb3 and Rd effectively reduced the size and the number of the polyps that accompanied with the downregulation of oncogenic signaling molecules (iNOS, STAT3/pSTAT3, Src/pSrc). Both the compounds improved the gut epithelium by promoting goblet and Paneth cells population and reinstating the E-cadherin and N-Cadherin expression. Mucosal immunity remodeled with increased in anti-inflammatory cytokines and reduced in pro-inflammatory cytokines in treated mice. All these changes were correlating with the promoted growth of beneficial bacteria such as Bifidobacterium spp., Lactobacillus spp., Bacteroides acidifaciens, and Bacteroides xylanisolvens. Whereas, the abundance of cancer cachexia associated bacteria, such as Dysgonomonas spp. and Helicobacter spp., was profoundly lower in Rb3/Rd-treated mice. In conclusion, ginsenosides Rb3 and Rd exerted anti-cancer effects by holistically reinstating mucosal architecture, improving mucosal immunity, promoting beneficial bacteria, and down-regulating cancer-cachexia associated bacteria.

Phylogenetic and functional analysis of gut microbiota of a fungus-growing higher termite: Bacteroidetes from higher termites are a rich source of β-glucosidase genes

Fungus-growing termites, their symbiotic fungi, and microbiota inhibiting their intestinal tract comprise a highly efficient cellulose-hydrolyzing system; however, little is known about the role of gut microbiota in this system. Twelve fosmid clones with β-glucosidase activity were previously obtained by functionally screening a metagenomic library of a fungus-growing termite, Macrotermes annandalei. Ten contigs containing putative β-glucosidase genes (bgl1-10) were assembled by sequencing data of these fosmid clones. All these contigs were binned to Bacteroidetes, and all these β-glucosidase genes were phylogenetically closed to those from Bacteroides or Dysgonomonas. Six out of 10 β-glucosidase genes had predicted signal peptides, indicating a transmembrane capability of these enzymes to mediate cellulose hydrolysis within the gut of the termites. To confirm the activities of these β-glucosidase genes, three genes (bgl5, bgl7, and bgl9) were successfully expressed and purified. The optimal temperature and pH of these enzymes largely resembled the environment of the host's gut. The gut microbiota composition of the fungus-growing termite was also determined by 454 pyrosequencing, showing that Bacteroidetes was the most dominant phylum. The diversity and the enzyme properties of β-glucosidases revealed in this study suggested that Bacteroidetes as the major member in fungus-growing termites contributed to cello-oligomer degradation in cellulose-hydrolyzing process and represented a rich source for β-glucosidase genes.

16S-rRNA-based analysis of bacterial diversity in the gut of fungus-cultivating termites (Microtermes and Odontotermes species)

The interaction between termites and their gut symbionts has continued to attract the curiosity of researchers over time. The aim of this study was to characterize and compare the bacterial diversity and community structure in the guts of three termites (Odontotermes somaliensis, Odontotermes sp. and Microtermes sp.) using 16S rRNA gene sequencing of clone libraries. Clone libraries were screened by restriction fragment length polymorphism and representative clones from O. somaliensis (100 out of 330 clones), Odontotermes sp. (100 out of 359 clones) and Microtermes sp. (96 out 336 clones) were sequenced. Phylogenetic analysis indicated seven bacterial phyla were represented: Bacteroidetes, Spirochaetes, Firmicutes, Proteobacteria, Synergistetes, Planctomycetes and Actinobacteria. Sequences representing the phylum Bacteroidetes (>60 %) were the most abundant group in Odontotermes while those of Spirochaetes (29 %) and Firmicutes (23 %) were the abundant groups in Microtermes. The gut bacterial community structure within the two Odontotermes species investigated here was almost identical at the phylum level, but the Microtermes sp. had a unique bacterial community structure. Bacterial diversity was higher in Odontotermes than in Microtermes. The affiliation and clustering of the sequences, often with those from other termites' guts, indicate a majority of the gut bacteria are autochthonous having mutualistic relationships with their hosts. The findings underscore the presence of termite-specific bacterial lineages, the majority of which are still uncultured.

First isolation of Dysgonomonas mossii from intestinal juice of a patient with pancreatic cancer

BACKGROUND

Dysgonomonas species were first designated in 2000. However, clinical infections due to this microorganism have rarely been described. Our aim was to present the first isolation of Dysgonomonas mossii from intestinal juice of a patient with pancreatic cancer.

METHODS

Predominantly appearing grayish-white colonies grown on chocolate and sheep blood agar plates were characterized morphologically by Gram stain, biochemically by automated instrument using Vitek II ID-GNB card together with commercially available kit systems, ID-Test HN-20 and API rapid ID 32A32A, and genetically by sequencing the 16S rRNA gene of the organism using a Taq DyeDeoxy Terminator Cycle Sequencing and a model 3100 DNA sequencer instrument. The isolate was further characterized by antimicrobial susceptibility using MicroFast 4J Panels and additional biochemical and physiological properties.

RESULTS

The isolate was finally identified as D. mossii from the findings of the morphological, cultural, and biochemical properties together with the comparative sequence of the 16S rRNA genes. The isolate was highly susceptible to many antibiotics but resistant to penicillins and cephems.

CONCLUSIONS

As D. mossii was rarely encountered in the clinical microbiology laboratory, it may be misidentified as an X-factor-dependent Haemophilus species due to its negative result for the porphyrin test. Accumulation of the case reports with the isolation of this species is expected to elucidate the infections due to D. mossii. The presence of D. mossii caused no significant clinical infection despite repeated isolations, as the patient had no conspicuous abdominal complaints. However, our report is a noteworthy and useful piece of information.