Acute cholecystitis accompanied by acute pancreatitis potentially caused by Dolosigranulum pigrum

Fatal Septic Shock Due to Dolosigranulum pigrum Bacteremia: a Case Report

We report the case of a 77-year-old Japanese woman with neuromyelitis optica spectrum disorder treated with 15 mg of prednisolone daily who presented with acute septic shock and altered consciousness due to Dolosigranulum pigrum bacteremia. Intravenous fluid and broad-spectrum antibiotics were initiated; however, the patient died shortly after admission. We performed 16S rRNA sequencing and analyzed the murJ gene. A phylogenetic tree constructed using the neighbor-joining method showed that the strain belonged to Clade C3, according to the Flores Ramos classification system. Although D. pigrum is a commensal of the upper respiratory tract and is rarely associated with infections, it can occasionally cause serious infections. Further clinical and bacteriological data are needed to provide an understanding of the pathogenicity and infections caused by this organism.

Dolosigranulum savutiense sp. nov., isolated from human upper respiratory samples collected in Botswana

Four strains (MSK211, MSK294T, MSK312, MSK433) of a novel Dolosigranulum species were cultured from nasopharyngeal swabs collected from mother-infant dyads in southern Botswana. These strains grew optimally on tryptic soy agar with 5% sheep blood solid medium and in fastidious bacteria broth. Colonies on tryptic soy agar with 5% sheep blood agar appeared grey or white with a flat, smooth surface and variable alpha haemolysis. Cells were Gram-positive, non-spore-forming, non-motile cocci that lacked catalase or oxidase activity. Major fatty acids were C16 : 0 (palmitic acid), C18 : 1 ω9c (oleic acid), and C18 : 0 (stearic acid). Analyses of 16S rRNA gene sequences identified these strains as belonging to the genus Dolosigranulum (family Carnobacteriaceae), which currently contains only a single validly published species (Dolosigranulum pigrum). Whole-genome sequencing revealed that the genomes of these strains are 1.98-2.07 Mbp in size and have a G+C content of 39.6-39.9 mol%. Comparisons of these genomes to publicly available genomes of D. pigrum yielded average nucleotide identities and in silico DNA-DNA hybridization values of 92.3-92.9% and 49.1-51.4%, respectively. These results indicate that these strains represent a novel species of Dolosigranulum, for which we propose the name Dolosigranulum savutiense sp. nov., with the type strain MSK294T (=DSM 117171T=JCM 36673T).

Successful Use of Phage and Antibiotics Therapy for the Eradication of Two Bacterial Pathogens from the Respiratory Tract of an Infant

Phage therapy can be a useful approach in a number of clinical cases associated with multidrug-resistant (MDR) bacterial infections. In this study, we describe a successful consecutive phage and antibiotic application to cure a 3-month-old girl suffering from severe bronchitis after tracheostomy. Bronchitis was associated with two bacterial agents, MDR Pseudomonas aeruginosa and a rare opportunistic pathogen Dolosigranulum pigrum. The phage cocktail "Pyobacteriophage" containing at least two different phages against isolated MDR P. aeruginosa strain was used via inhalation and nasal drops. Topical application of the phage cocktail removed most of P. aeruginosa cells and contributed to a change in the antimicrobial resistance profile of surviving P. aeruginosa cells. As a result, it became possible to choose and administer an appropriate antibiotic that was effective against both infectious agents. Complete recovery of the infant was recorded.

Native mitral valve infective endocarditis due to Dolosigranulum pigrum

Dolosigranulum pigrum is an anaerobic, gram-positive coccus rarely identified as a pathogenic organism. However, case reports have suggested D. pigrum as a causative pathogen in bacteremia, nosocomial pneumonia, ventilator-associated pneumonia, synovitis, cholecystitis, and ophthalmologic infections. Herein, we present the first case of Dolosigranulum pigrum causing native mitral valve infective endocarditis. With the exception of erythromycin, the isolate displayed favorable minimum inhibitory concentrations (MIC) to all other antibiotics tested, including beta-lactams, levofloxacin, and vancomycin. The patient was successfully treated with a 6-week course of intravenous (IV) ceftriaxone followed by robotically assisted cardiac valve repair.

[Dolosigranulum pigrum in corneal abscess]

Dolosigranulum pigrum is a gram-positive, facultatively anaerobic coccus, which is part of the oral and upper respiratory tract microbiota. Although reports of infections by this microorganism are scarce, it has been associated with a wide spectrum of infectious diseases. The case of an elderly man with a lower corneal abscess, in which Dolosigranulum pigrum was isolated, is described. The microorganism was identified by mass spectrometry (MALDI-TOF MS) and by the sequencing of the 16S rRNA gene. Furthermore, the presumptive identification of the causative agent was achieved by using key phenotypic tests such as the cluster arrangement in Gram stain, the negative catalase test, the production of pyrrolidonyl arylamidase and leucine aminopeptidase activity, the growth in 6.5% NaCl and esculin hydrolysis. The data from the literature (and the present case) support the association of the microorganism with ocular infections, which often take a destructive course, mainly in elderly patients.

Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome

Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.

Prevalences and characteristics of cultivable nasal bacteria isolated from preclinical medical students

OBJECTIVES

Commensal bacteria in the nasal cavity may act as opportunistic pathogens that cause infections under certain conditions. Screening for commensal bacteria in the nasal cavity may aid in understanding their roles in microbiota balance and preventing potential infections.

METHODS

Nasal samples were collected from healthy preclinical medical students and used to inoculate various bacterial culture media, by means of the WaspLab microbiology automated system. Bacterial colonies were then identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry. Antibiotic resistance phenotypes of Staphylococcus aureus were determined by antibiotic susceptibility tests.

RESULTS

In total, 549 bacterial strains were isolated from 161 participants. These strains included the following genera: Staphylococcus, Streptococcus, Corynebacterium, Dolosigranulum, Bacillus, Micrococcus, Haemophilus, Neisseria, Moraxella, Pseudomonas, and members of Enterobacteriaceae (e.g., Escherichia, Klebsiella, Citrobacter, Enterobacter, and Serratia). Approximately 25.5% of students were carriers of S. aureus; most S. aureus isolates were resistant to penicillin, erythromycin, and clindamycin. The prevalence of methicillin-resistant S. aureus in nasal samples was 4.3%.

CONCLUSIONS

A diverse group of nasal commensal bacteria inhabited our population of healthy volunteers. These data can improve comprehension of the potential roles of these nasal commensal bacteria in regulating microbiota balance and promoting or mitigating potential future infections.

First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies

Dolosigranulum pigrum is a quite recently discovered Gram-positive coccus. It has gained increasing attention due to its negative correlation with Staphylococcus aureus, which is one of the most successful modern pathogens causing severe infections with tremendous morbidity and mortality due to its multiple resistances. As the possible mechanisms behind its inhibition of S. aureus remain unclear, a genome-scale metabolic model (GEM) is of enormous interest and high importance to better study its role in this fight. This article presents the first GEM of D. pigrum, which was curated using automated reconstruction tools and extensive manual curation steps to yield a high-quality GEM. It was evaluated and validated using all currently available experimental data of D. pigrum. With this model, already predicted auxotrophies and biosynthetic pathways could be verified. The model was used to define a minimal medium for further laboratory experiments and to predict various carbon sources' growth capacities. This model will pave the way to better understand D. pigrum's role in the fight against S. aureus.

Dolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota

Staphylococcus aureus and Streptococcus pneumoniae infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify Dolosigranulum pigrum as a benign bacterium present when adults are free of S. aureus or when children are free of S. pneumoniae. Here, we validated these in vivo associations with functional assays. We found that D. pigrum inhibited S. aureusin vitro and, together with a specific nasal Corynebacterium species, also inhibited S. pneumoniae. Furthermore, genomic analysis of D. pigrum indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate D. pigrum as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude S. aureus and/or S. pneumoniae.

Multiple epidemiological studies identify Dolosigranulum pigrum as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species Staphylococcus aureus and Streptococcus pneumoniae. Using a multipronged approach to gain new insights into D. pigrum function, we observed phenotypic interactions and predictions of genomic capacity that support the idea of a role for microbe-microbe interactions involving D. pigrum in shaping the composition of human nasal microbiota. We identified in vivo community-level and in vitro phenotypic cooperation by specific nasal Corynebacterium species. Also, D. pigrum inhibited S. aureus growth in vitro, whereas robust inhibition of S. pneumoniae required both D. pigrum and a nasal Corynebacterium together. D. pigruml-lactic acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that D. pigrum has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with D. pigrum relying on its human host and on cocolonizing bacteria for key nutrients. Further, the accessory genome of D. pigrum harbored a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions. These new insights into D. pigrum’s functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments.

IMPORTANCEStaphylococcus aureus and Streptococcus pneumoniae infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify Dolosigranulum pigrum as a benign bacterium present when adults are free of S. aureus or when children are free of S. pneumoniae. Here, we validated these in vivo associations with functional assays. We found that D. pigrum inhibited S. aureusin vitro and, together with a specific nasal Corynebacterium species, also inhibited S. pneumoniae. Furthermore, genomic analysis of D. pigrum indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate D. pigrum as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude S. aureus and/or S. pneumoniae.

Dolosigranulum pigrum: Predicting Severity of Infection

In this report, we describe a case of a 61-year-old male patient who had the bacterium Dolosigranulum pigrum growing in a blood culture. It was susceptible to ampicillin, ceftriaxone, levofloxacin, and vancomycin but was intermediately resistant to erythromycin. The patient did not have a negative outcome as a consequence of this bacterium, which retrospectively could have been predicted based on the epidemiological data within the patient's profile. 

Accuracy of ultrasound in the diagnosis of acute cholecystitis with coexistent acute pancreatitis

PURPOSE

Acute cholecystitis and pancreatitis are acute forms of cholecystolithiasis. The presence of acute cholecystitis can lead to important changes in therapy in the early course of acute pancreatitis. The aim of this study was to identify the accuracy of ultrasonography in diagnosing acute cholecystitis with coexistent acute pancreatitis.

METHODS

Subjects were all those patients admitted to our hospital with a diagnosis of acute pancreatitis between 1998 and 2015 who underwent cholecystectomy within 15 days of the ultrasonography performed on admittance. Patient data were analyzed retrospectively to compare the ultrasound findings with the pathological findings of the resected gallbladders. Patients were allocated to two groups according to the signs of acute cholecystitis on ultrasonography: group 1 negative and group 2 positive.

RESULTS

One hundred and twenty patients were enrolled in the study: 77 in group 1 and 43 in group 2. Similar results were found for the two groups with respect to the pathological diagnosis of acute cholecystitis, i.e., 31.2 % for group 1 and 27.9 % for group 2. Analysis indicated that there was no correlation between the ultrasonography data and pathological findings (p = 0.708).

CONCLUSIONS

On the basis of our study, ultrasound findings alone cannot be used to accurately diagnose acute cholecystitis in the setting of acute pancreatitis.

Dolosigranulum pigrum keratitis: a three-case series

Background

Dolosigranulum pigrum is a commensal inhabitant of the upper respiratory tract suspected to be responsible for ocular infections but no well-described case of D. pigrum corneal infection has been reported. Herein culture and PCR-sequencing-based investigations of corneal scraping specimens confirmed D. pigrum keratitis in three patients.

Case presentation

Three elderly patients presented with unilateral keratitis. None was a corneal-contact lens wearer, one had previous cataract surgery and another suffered rheumatoid arthritis sicca syndrome. Culturing the corneal scraping specimen was positive for two cases and PCR-sequencing of bacterial 16S rDNA in the presence of negative controls identified D. pigrum in three cases. The two D. pigrum isolates were in-vitro susceptible to penicillin G, amoxicillin, doxycycline, rifampicin and gentamicin. In all cases, surgical treatment of corneal thinning was necessary, but corneal perforation occurred in two cases despite intensive antimicrobial treatment with ticarcillin, gentamicin and vancomycin or levofloxacin eye drops leading to enucleation in one case.

Conclusions

D. pigrum is the likely cause of corneal infection in three patients, with effective antibiotic treatment in two patients.

Infectious diseases and the gallbladder

Infections of the gastrointestinal tract can often involve the gallbladder. Infection probably plays a role in the formation of gallstones but is more commonly thought to contribute to acute illness in patients. Acute calculous cholecystitis caused by an impacted gallstone is often complicated by secondary bacterial infection and is a major cause of morbidity and even mortality in patients. A wide variety of organisms can be associated with acute acalculous cholecystitis, a less common but potentially more severe form of acute cholecystitis. This review focuses on infections and their role in the above-mentioned processes involving the gallbladder.

Dolosigranulum pigrum causing biomaterial-associated arthritis

Dolosigranulum pigrum is a gram-positive, catalase-negative bacteria rarely associated with disease. We report a case of biomaterial-associated arthritis in an immunocompetent patient caused by D. pigrum. The organism was isolated from a synovial biopsy specimen and its identity confirmed by 16S rRNA gene sequencing.

Dolosigranulum pigrum causing nosocomial pneumonia and septicemia

We report a case of non-ventilator-associated nosocomial pneumonia and septicemia due to Dolosigranulum pigrum, a rare gram-positive opportunistic pathogen. The organism was isolated from bronchoalveolar lavage fluid and blood of a debilitated patient. D. pigrum was identified after 16S rRNA gene sequencing.

Ventilator-associated pneumonia caused by Dolosigranulum pigrum

Dolosigranulum pigrum is an unusual gram-positive catalase-negative coccus. It was isolated, only after prolonged incubation, from bronchial secretions from a patient with ventilator-associated pneumonia. The patient responded well to antimicrobial therapy. Identification was done by 16S rRNA DNA sequence analysis, but it can be done with relatively simple phenotypic tests.