Outbreak of carbapenemase-producing Citrobacter farmeri in an intensive care haematology department linked to a persistent wastewater reservoir in one hospital room, France, 2019 to 2022.

In 2019-2022, a prolonged outbreak of oxacillinase (OXA)-48-producing Citrobacter farmeri due to a persistent environmental contamination, occurred in our haematology intensive care unit. In April 2019, we isolated OXA-48-producing C. farmeri from rectal samples of two patients in weekly screenings. The cases had stayed in the same hospital room but 4 months apart. We screened five patients who had stayed in this room between the two cases and identified a third case. Over the following 3 years, five other cases were detected, the last case in September 2022. In total, eight cases were detected: seven colonised with the bacterium and one infected with a lethal outcome. All cases stayed in the same hospital room. We detected OXA-48-producing C. farmeri from a shower, washbasin drains and wastewater drainage of the bathroom of the hospital room. Molecular typing confirmed that all C. farmeri isolates from the environment and the cases were indistinguishable. Despite bundle measures to control the outbreak, the bacterium persisted in the system, which resulted in transmission to new patients. A design defect in the placement of wastewater drains contributed to the persistence and proliferation of the bacterium. The room was closed after the last case and the bathroom rebuilt.

Xpert MTB/RIF Ultra Trace Results: Decision Support for the Treatment of Extrapulmonary Tuberculosis in Low TB Burden Countries.

OBJECTIVES: Extrapulmonary tuberculosis (EPTB) can be difficult to diagnose, especially in severe forms. The Xpert MTB/RIF Ultra test introduced an additional category called trace to reference very small amounts of Mycobacterium tuberculosis complex (MTBC) DNA. The objective of our multicenter study was to evaluate whether the trace result on an extrapulmonary (EP) sample is a sufficient argument to consider diagnosing tuberculosis and starting treatment, even in severe cases. METHODS: A retrospective, multicenter cohort study was conducted from 2018 to 2022. Patients strongly suspected of EPTB with a trace result on an EP specimen were included. Hospital records were reviewed for clinical, treatment, and paraclinical data. RESULTS: A total of 52 patients were included, with a severe form in 22/52 (42.3%) cases. Culture was positive for MTBC in 33/46 (71.7%) cases. Histological analysis showed granulomas in 36/45 (80.0%) cases. An Ultra trace result with a presumptive diagnosis of TB led to the decision to treat 41/52 (78.8%) patients. All patients were started on first-line anti-TB therapy (median duration of 6.1 months), with a favorable outcome in 31/35 (88.6%) patients. The presence of a small amount of MTBC genome in EPTB is a sufficient argument to treat patients across a large region of France.

In vitro susceptibility of nonfermenting Gram-negative rods to meropenem-vaborbactam and delafloxacin.

Aim: Meropenem-vaborbactam and delafloxacin activities were not assessed against Achromobacter spp. (Achr), Burkholderia cepacia complex (Bcc) and Stenotrophomonas maltophilia (Smal). Methodology: A total of 106 Achr, 57 Bcc and 100 Smal were tested with gradient diffusion test of meropenem-vaborbactam, delafloxacin and comparators. Results: Meropenem-vaborbactam MIC50 were 4 µg/ml for Achr, 1 µg/ml for B. cepacia, 2 µg/ml for B. cenocepacia and B. multivorans, and 32 µg/ml for Smal. Delafloxacin MIC50 were 4 µg/ml for Achr, 0.25 µg/ml for B. cepacia and B. multivorans, 2 µg/ml for B. cenocepacia, and 0.5 µg/m for Smal. meropenem-vaborbactam MICs were fourfold lower than meropenem for 28.3% Achr, 77.2% B. cepacia, 53.8% B. cenocepacia and 77.2% B. multivorans. Conclusion: Meropenem-vaborbactam and delafloxacin are in vitro active against Bcc and Achr.

We assess the efficacy of two new antibiotics, meropenem­vaborbactam and delafloxacin, to kill rarely encountered bacteria. These bacteria, Achromobacter, Burkholderia and Stenotrophomonas maltophilia, mainly cause respiratory tract infections. Both antibiotics are found active against Achromobacter and Burkholderia, but not S. maltophilia.

An upgraded version of carbapenem inactivation method to detect Bacteroides fragilis carbapenemase.

An increase of carbapenemase-producing Bacteroides fragilis infections is observed. To detect such a resistance in B. fragilis, several tests exist that are expensive or show poor sensitivity and specificity. Therefore, we upgraded the Anaerobic Carbapenem Inactivation Method (Ana-CIM) to easily screen for carbapenemase-producing B. fragilis. The presence of carbapenemase cfiA gene was identified in 50 B. fragilis isolates by PCR. We modified the Ana-CIM by (1) increasing the bacterial inoculum, and (2) measuring the differences in diameter between the negative control and the testing disc. We correctly classified the cfiA-negative and positive isolates and could define a cut-off of positivity at 2 mm. Our modified Ana-CIM allowed to correctly discriminate the 31 cfiA-positive with meropenem MICs ranging from 1 to > 32 µg/mL. We anticipate that our modified Ana-CIM could be used in most clinical laboratories to easily screen for carbapenemase-producing B. fragilis, even at low levels.

Parabacteroides distasonis Properties Linked to the Selection of New Biotherapeutics.

Dysbiotic microbiota is often associated with health issues including inflammatory bowel disease or ulcerative colitis. In order to counterbalance host disorder caused by an alteration in the gut composition, numerous studies have focused on identifying new biotherapeutic products (NBPs). Among the promising NBPs is Parabacteroides distasonis, a gut microbiota member part of the core microbiome that recently has received much attention due to the numerous beneficial properties it brings to its host. In this study, the properties linked to the selection of NBPs were screened in 14 unrelated P. distasonis strains, including resistance to gastric conditions, adherence (Caco-2 model), transepithelial resistance (Caco-2 model), and immunomodulation, on nontreated and LPS-stimulated cells (HT-29 and peripheral blood mononuclear cells (PBMCs)). This approach allowed for the identification of five strains that combined almost all the in vitro biotherapeutic properties tested. However, all the P. distasonis strains induced the overproduction of proinflammatory cytokines on PBMCs, which was counteracted by the overproduction of the anti-inflammatory cytokines. Among these five strains, two particularly retained our attention as a potential NBP, by showing strong health-promoting function, the lowest overproduction of proinflammatory cytokines on PBMCs, and no detrimental effect on the host.

In Silico Study of Cell Surface Structures of Parabacteroides distasonis Involved in Its Maintenance within the Gut Microbiota.

The health-promoting Parabacteroides distasonis, which is part of the core microbiome, has recently received a lot of attention, showing beneficial properties for its host and potential as a new biotherapeutic product. However, no study has yet investigated the cell surface molecules and structures of P. distasonis that allow its maintenance within the gut microbiota. Moreover, although P. distasonis is strongly recognized as an intestinal commensal species with benefits for its host, several works displayed controversial results, showing it as an opportunistic pathogen. In this study, we reported gene clusters potentially involved in the synthesis of capsule, fimbriae-like and pili-like cell surface structures in 26 P. distasonis genomes and applied the new RfbA-typing classification in order to better understand and characterize the beneficial/pathogenic behavior related to P. distasonis strains. Two different types of fimbriae, three different types of pilus and up to fourteen capsular polysaccharide loci were identified over the 26 genomes studied. Moreover, the addition of data to the rfbA-type classification modified the outcome by rearranging rfbA genes and adding a fifth group to the classification. In conclusion, the strain variability in terms of external proteinaceous structure could explain the inter-strain differences previously observed of P. distasonis adhesion capacities and its potential pathogenicity, but no specific structure related to P. distasonis beneficial or detrimental activity was identified.

Clostridium haemolyticum Infection: A Cause of Hemolytic Anemia in a Patient with Bone Marrow Necrosis.

Clostridium haemolyticum is a sporulating Gram-positive anaerobic rod that is considered to be one of the most fastidious and oxygen-sensitive anaerobes. It is a well-known animal pathogen and the cause of bacillary hemoglobinuria primarily in cattle. To date, human infections caused by C. haemolyticum have been reported in three patients with malignant underlying diseases. We present herein the case of a 30-year-old obese woman with no significant past medical history who developed bacteremia caused by C. haemolyticum with massive intravascular hemolysis associated with bone marrow necrosis and acute renal failure. Because of subculture failure, the diagnosis was made on the basis of 16S rDNA sequencing and next-generation sequencing. The patient, who had been afebrile for 20 days after a 17-day-course of antibiotics, experienced a second bacteremic episode caused by C. haemolyticum. After having been successfully treated for 42 days with clindamycin and amoxicillin-clavulanic acid, the patient developed acute myeloid leukemia as a result of bone marrow regeneration. Although uncommon in humans, infections caused by C. haemolyticum are severe and should be considered in a febrile patient who has severe hemolytic anemia. This case also highlights the importance of using molecular techniques for the identification of this fastidious anaerobic organism.

Surface Properties of Parabacteroides distasonis and Impacts of Stress-Induced Molecules on Its Surface Adhesion and Biofilm Formation Capacities.

The gut microbiota is a complex and dynamic ecosystem whose balance and homeostasis are essential to the host's well-being and whose composition can be critically affected by various factors, including host stress. Parabacteroides distasonis causes well-known beneficial roles for its host, but is negatively impacted by stress. However, the mechanisms explaining its maintenance in the gut have not yet been explored, in particular its capacities to adhere onto (bio)surfaces, form biofilms and the way its physicochemical surface properties are affected by stressing conditions. In this paper, we reported adhesion and biofilm formation capacities of 14 unrelated strains of P. distasonis using a steam-based washing procedure, and the electrokinetic features of its surface. Results evidenced an important inter-strain variability for all experiments including the response to stress hormones. In fact, stress-induced molecules significantly impact P. distasonis adhesion and biofilm formation capacities in 35% and 23% of assays, respectively. This study not only provides basic data on the adhesion and biofilm formation capacities of P. distasonis to abiotic substrates but also paves the way for further research on how stress-molecules could be implicated in P. distasonis maintenance within the gut microbiota, which is a prerequisite for designing efficient solutions to optimize its survival within gut environment.

Algorithm for rational use of Film Array Pneumonia Panel in bacterial coinfections of critically ill ventilated COVID-19 patients.

The FilmArray Pneumonia Panel has proven to be an effective tool for rapid detection of main respiratory pathogens. However, its rational use needs appropriate knowledge and formation regarding its indication and interpretation. Herein, we provide some advices to help with success of its daily routine use, particularly in critically ill ventilated COVID-19 patients. Clinical Trial registration number: NCT04453540.

A New Look at the Genus Solobacterium: A Retrospective Analysis of Twenty-Seven Cases of Infection Involving S. moorei and a Review of Sequence Databases and the Literature.

Solobacterium moorei is an anaerobic Gram-positive bacillus present within the oral and the intestinal microbiota that has rarely been described in human infections. Besides its role in halitosis and oral infections, S. moorei is considered to be an opportunistic pathogen causing mainly bloodstream and surgical wound infections. We performed a retrospective study of 27 cases of infections involving S. moorei in two French university hospitals between 2006 and 2021 with the aim of increasing our knowledge of this unrecognized opportunistic pathogen. We also reviewed all the data available in the literature and in genetic and metagenomic sequence databases. In addition to previously reported infections, S. moorei had been isolated from various sites and involved in intra-abdominal, osteoarticular, and cerebral infections more rarely or not previously reported. Although mostly involved in polymicrobial infections, in seven cases, it was the only pathogen recovered. Not included in all mass spectrometry databases, its identification can require 16S rRNA gene sequencing. High susceptibility to antibiotics (apart from rifampicin, moxifloxacin, and clindamycin; 91.3%, 11.8%, and 4.3% of resistant strains, respectively) has been noted. Our global search strategy revealed S. moorei to be human-associated, widely distributed in the human microbiota, including the vaginal and skin microbiota, which may be other sources for infection in addition to the oral and gut microbiota.

Relations of Psychosocial Factors and Cortisol with Periodontal and Bacterial Parameters: A Prospective Clinical Study in 30 Patients with Periodontitis Before and After Non-Surgical Treatment.

(1) Background: The progression of periodontitis, induced by polymicrobial dysbiosis, can be modified by systemic or environmental factors such as stress or anxiety affecting host response. The purpose of this study is to evaluate the potential associations between psychosocial factors scores or salivary cortisol levels with clinical periodontal parameters and bacterial environment in patients with periodontitis; (2) Methods: Subgingival microbiota was collected in two pathological and one healthy sites from thirty diseased patients (before/after scaling and root planing (SRP)) and from one healthy site from thirty control patients. Usual clinical periodontal parameters were recorded, and a saliva sample was harvested. Patients completed stress and anxiety self-assessment questionnaires. Cortisol concentrations were determined by ELISA and bacteria were identified by PCR; (3) Results: No correlation between salivary cortisol and the stress-anxiety self-declared was found (p > 0.05), but high concentrations of this molecule were associated positively and linearly with periodontal pocket depth (p = 0.04). It appeared that certain psychosocial stressors are associated with a modulation of the bacterial colonization of pockets of diseased group (before/after SRP), notably concerning Tannerella forsythia (p = 0.02), Porphyromonas gingivalis (p = 0.03), Fusobacterium nucleatum (p = 0.049) and Campylobacter rectus (p = 0.01). (4) Conclusion: This study reveals associations between bacteria colonization and psychosocial parameters in periodontitis that needs to be further investigated.

Impact of a Model Used to Simulate Chronic Socio-Environmental Stressors Encountered during Spaceflight on Murine Intestinal Microbiota.

During deep-space travels, crewmembers face various physical and psychosocial stressors that could alter gut microbiota composition. Since it is well known that intestinal dysbiosis is involved in the onset or exacerbation of several disorders, the aim of this study was to evaluate changes in intestinal microbiota in a murine model used to mimic chronic psychosocial stressors encountered during a long-term space mission. We demonstrate that 3 weeks of exposure to this model (called CUMS for Chronic Unpredictable Mild Stress) induce significant change in intracaecal ß-diversity characterized by an important increase of the Firmicutes/Bacteroidetes ratio. These alterations are associated with a decrease of Porphyromonadaceae, particularly of the genus Barnesiella, a major member of gut microbiota in mice and humans where it is described as having protective properties. These results raise the question of the impact of stress-induced decrease of beneficial taxa, support recent data deduced from in-flight experimentations and other ground-based models, and emphasize the critical need for further studies exploring the impact of spaceflight on intestinal microbiota in order to propose strategies to countermeasure spaceflight-associated dysbiosis and its consequences on health.

Comparison of sTREM-1 and associated periodontal and bacterial factors before/after periodontal therapy, and impact of psychosocial factors.

AIM: The immune receptor triggering receptor expressed on myeloid cell-1 (TREM-1) is responsible for an amplification of the immuno-inflammatory response in inflammatory diseases. Its role in the aetiopathogenesis of periodontitis is underexplored. The aim of this case-control and before-after study was to determine the evolution of soluble form of TREM-1 (sTREM-1) concentrations after scaling and root planing (SRP), and its prognostic value and evaluate associated microbial, periodontal and psychosocial factors. METHODS: Gingival crevicular fluid was collected in two pathological sites (periodontal pocket depth (PPD) ≥ 5 mm) and one healthy site (PPD ≤ 3 mm) from thirty periodontitis patients (before/after SRP), and in one healthy site from thirty controls (patients without periodontal disease). Each patient filled-in stress/anxiety self-assessment questionnaires and provided a saliva sample. Diseased patients were followed for a total of 13-15 weeks in initial periodontal treatment. sTREM-1 and salivary cortisol levels were determined by ELISA and periodontopathogens by PCR. RESULTS: Before SRP, higher crevicular sTREM-1 levels were positively associated with some increased clinical parameters (Plaque Index, tooth mobility, bleeding on probing, p < .05) and inversely with Aggregatibacter actinomycetemcomitans abundance (p = .03). No correlation with psychological factors nor cortisol was found with salivary sTREM-1 concentrations. After SRP, crevicular sTREM-1 levels decreased (p < .001) and were not linked to a PPD decrease but remained higher in pathological than in healthy sites (p < .001). Higher concentrations were also found out in unimproved sites (no change or increase in PPD) compared to improved ones (p = .02). Higher sTREM-1 levels were associated with Porphyromonas gingivalis, Treponema denticola and Campylobacter rectus in pathological sites after SRP (p < .05). CONCLUSION: Crevicular sTREM-1 level decreased after SRP but did not appear to be a site outcome predictive factor of periodontal healing and remained an inflammatory parameter.

Bone marrow vs Wharton's jelly mesenchymal stem cells in experimental sepsis: a comparative study.

BACKGROUND: The use of mesenchymal stem cells (MSCs) is being extensively studied in clinical trials in the setting of various diseases including diabetes, stroke, and progressive multiple sclerosis. The unique immunomodulatory properties of MSCs also point them as a possible therapeutic tool during sepsis and septic shock, a devastating syndrome associated with 30-35% mortality. However, MSCs are not equal regarding their activity, depending on their tissue origin. Here, we aimed at comparing the in vivo properties of MSCs according to their tissue source (bone marrow (BM) versus Wharton's jelly (WJ)) in a murine cecal ligation and puncture (CLP) model of sepsis that mimics a human peritonitis. We hypothesized that MSC properties may vary depending on their tissue source in the setting of sepsis. METHODS: CLP, adult, male, C57BL/6 mice were randomized in 3 groups receiving respectively 0.25 × 106 BM-MSCs, 0.25 × 106 WJ-MSCs, or 150 µL phosphate-buffered saline (PBS) intravenously 24 h after the CLP procedure. RESULTS: We observed that both types of MSCs regulated leukocyte trafficking and reduced organ dysfunction, while only WJ-MSCs were able to improve bacterial clearance and survival. CONCLUSION: This study highlights the importance to determine the most appropriate source of MSCs for a given therapeutic indication and suggests a better profile for WJ-MSCs during sepsis.

Hypergravity disrupts murine intestinal microbiota.

During spaceflight, organisms are subjected to various physical stressors including modification of gravity (G) that, associated with lifestyle, could lead to impaired immunity, intestinal dysbiosis and thus potentially predispose astronauts to illness. Whether space travel affects microbiota homeostasis has not been thoroughly investigated. The aim of this study was to evaluate changes in intestinal microbiota and mucosa in a ground-based murine model consisting in a 21-days confinement of mice in a centrifuge running at 2 or 3G. Results revealed an increased α-diversity and a significant change in intracaecal ß-diversity observed only at 3G, with profiles characterized by a decrease of the Firmicutes/Bacteroidetes ratio. Compared to 1G microbiota, 12.1% of the taxa were significantly impacted in 3G microbiota, most of them (78%) being enriched. This study shows a G-level-dependent disruption of intracaecal microbiota, without alteration of mucosal integrity. These first data reinforce those recently obtained with in-flight experimentations or microgravity models, and emphasize the critical need for further studies exploring the impact of spaceflight on intestinal microbiota in order to optimize long-term space travel conditions.

Hepatic abscess due to Dialister pneumosintes - A case report.

Dialister pneumosintes is an obligate anaerobic Gram-negative rod associated with infections of the oral cavity. We report on a previously healthy, 51-year-old woman who presented with a liver abscess caused by Dialister pneumosintes as a complication of a dental abscess. The microorganism was identified by using a broad-range bacterial 16S rRNA gene PCR in the liver exudate. The patient was cured after abscess drainage and 4-week antibiotic treatment. Our case highlights the importance of a good history and physical examination when taking care of patients admitted for pyogenic liver abscess.

A case report of Guillain Barré syndrome revealing underlying infective endocarditis due to Cardiobacterium hominis.

RATIONALE: Guillain-Barré syndrome (GBS) is an acute inflammatory polyradiculoneuropathy presumed to result from an infection-triggered autoimmune reaction. PATIENT CONCERNS: This paper describes a 53-year-old man admitted to hospital for deterioration of his general condition. DIAGNOSIS: He developed GBS, confirmed by lumbar puncture and electromyogram, which recovered after intravenous immunoglobulins. A grade 2 aortic regurgitation was detected by transthoracic echocardiography upon diagnosis of GBS, but in the absence of fever, no further investigations were conducted. A few weeks later, the patient presented with fever and infective endocarditis (IE) was diagnosed after the identification of vegetation on the aortic valve with transesophageal echocardiography. The etiologic agent was identified as Cardiobacterium hominis based on 3 positive blood cultures and DNA detection in valvular material. INTERVENTIONS: IE was cured with a 6-week course of antibiotics and aortic valve replacement. OUTCOMES: The patient completely recovered from Guillain-Baré syndrome and IE. LESSONS: This case of GBS associated with C hominis endocarditis, emphasizes the importance of blood cultures and transesophageal echocardiography for the detection of IE and highlights the insidious nature of C hominis endocarditis which is often diagnosed late.

A sequence database analysis of 5-nitroimidazole reductase and related proteins to expand knowledge on enzymes responsible for metronidazole inactivation.

nim genes are associated, in combination with other factors, with acquired resistance to metronidazole (MTZ) in anaerobes. These genes encode 5-nitroimidazole reductase enzymes (Nim proteins) that reduce MTZ into an inactive compound. Eleven variants (nimA to nimK) are currently described in anaerobes with either a chromosomal or a plasmidic location. Mostly found in members of the Bacteroides fragilis group, nim genes were demonstrated in anaerobic taxa outside the phylum Bacteroidetes. Nitroreductase enzymes, weakly related to those found in Bacteroidetes but associated with MTZ inactivation, were also characterized both in anaerobic and non-anaerobic taxa. Published data only poorly reflect the growing number of data from cultivation-independent studies and sequences deposited in databases. Considering this limitation, we performed herein an analysis of the sequence databases with the aim to increase the current knowledge on Nim protein distribution and diversity. The 250 sequences the most closely related to the 11 known Nim proteins were selected and analyzed for identity level and phylogenetic relationships with Nim A to K proteins. The analysis revealed a larger diversity of anaerobic species harboring known Nim proteins than that currently described in the literature. Putative new variants of known Nim proteins and novel Nim proteins were found. In addition, nitroreductase proteins and homologs related to the pyridoxamine 5'-phosphate oxidase family were found in highly diverse anaerobic and aerobic taxa of human but also animal and environmental origin. On the other hand, we found a very low number of sequences recovered from metagenomic studies. Considering the different databases currently available to identify antimicrobial resistance genes (ARG) among metagenomic sequences, we hypothesized that this may, at least in part, be related to the incompleteness of ARG databases because none of them includes the 11 described nim genes at the time of our study. Both the wide distribution of proteins with potential MTZ inactivation ability within the bacterial world and a wider diversity of Nim determinants than expected from published literature is underlined in this sequence database analysis.

Metronidazole resistance and nim genes in anaerobes: A review.

Acquired resistance to metronidazole, a 5-nitroimidazole drug largely used worldwide in the empirical treatment of infections caused by anaerobes, is worrisome, especially since such resistance has been described in multidrug-resistant anaerobic bacteria. In anaerobes, acquired resistance to metronidazole may be due to a combination of various and complex mechanisms. Among them, nim genes, possibly located on mobile genetic elements, encode nitro-imidazole-reductases responsible for drug inactivation. Since the first description of Nim proteins about 25 years ago, more nim genes have been identified; currently 11 nim genes are known (nimA to nimK). Mostly reported in Bacteroides fragilis group isolates, nim genes are now described in a variety of anaerobic genera encompassing the 4 main groups of Gram-negative and Gram-positive bacilli and cocci, with variable expression ranging from phenotypically silent to low-level or high-level resistance to metronidazole. This review describes the trends of metronidazole resistance rates among anaerobes over the past 20 years and summarizes current knowledge on mechanisms involved in this resistance. It also provides an update on the phylogenetic and geographical distribution of nim genes, the mechanisms involved in their expression and regulation, and their role in metronidazole resistance.