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.

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.

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.

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.

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.

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.

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.

Evaluation of the Vitek MS and the MALDI Biotyper systems for the identification of less commonly isolated but clinically relevant anaerobes and facultative anaerobes.

The Vitek MS and MALDI Biotyper systems were evaluated for the identification of 221 strains belonging to less commonly isolated anaerobes and facultative anaerobes. Identifications were performed using direct deposit (DD), on-target extraction (FA) and full extraction (EXT). After DD, 29.9% and 34.3% of Gram-positive isolates (n = 137) as well as 36.9% and 58.3% of Gram-negative isolates (n = 84) were identified at the species-level with the Vitek-MS and the Biotyper system, respectively. The rates of correct species identification with the Biotyper system were significantly increased after extraction for Gram-positive isolates (FA: 75.2%, EXT: 78.1%) and Gram-negative isolates (FA: 72.6%, EXT: 78.6%). Extraction permitted to achieve higher correct species identification rates only for Gram-positive isolates (FA: 35.8%, EXT: 36.5%) with the Vitek MS. Thus, the accuracy of both systems needs to be further increased by expanding the databases. In the meantime, we recommend using a preliminary extraction step to obtain reliable results at least for the identification of Gram positive anaerobic bacteria with both systems.

Comparison of Vitek MS and MALDI Biotyper for Identification of Actinomycetaceae of Clinical Importance.

The Vitek MS in vitro diagnostic (IVD) and MALDI Biotyper IVD systems were evaluated for the identification of 158 strains of Actinomycetaceae. Correct species-level identification rates of 60.7% and 58.2% were obtained with the Vitek MS system after direct deposit and with the MALDI Biotyper system after on-plate formic acid treatment, respectively.

Discrimination between native and Tn6010-associated oqxAB in Klebsiella spp., Raoultella spp., and other Enterobacteriaceae by using a two-step strategy.

We developed a two-step PCR-based strategy to detect genes encoding OqxAB, allowing a specific assignment of Tn6010-associated oqxAB in Enterobacteriaceae. Chromosomal location in this setup was confirmed by hybridization with I-CeuI-restricted genomes. This approach led us to find that Klebsiella sp. and Raoultella sp. reference strains chromosomally carried oqxAB.

Soluble TREM-like transcript-1 regulates leukocyte activation and controls microbial sepsis.

The triggering receptor expressed on myeloid cells (TREM)-1 plays a crucial role during the onset of sepsis by amplifying the host immune response. The TREM-like transcript-1 (TLT-1) belongs to the TREM family, is selectively expressed on activated platelets, and is known to facilitate platelet aggregation through binding to fibrinogen. In this study, we show that a soluble form of TLT-1 is implicated in the regulation of inflammation during sepsis by dampening leukocyte activation and modulating platelet-neutrophil crosstalk. A 17-aa sequence of the TLT-1 extracellular domain (LR17) is responsible for this activity through competition with the TREM-1 ligand. Whereas early or late LR17 treatment of septic mice improves survival, treml-1(-/-) animals are highly susceptible to polymicrobial infection. The present findings identify platelet-derived soluble TLT-1 as a potent endogenous regulator of sepsis-associated inflammation and open new therapeutic perspectives. We anticipate soluble TLT-1 to be important in regulating leukocyte activation during other noninfectious inflammatory disorders.

Characterization of a new blaOXA-48-carrying plasmid in Enterobacteriaceae.

In this work, we characterized a new, 160-kb, blaOXA-48-harboring IncL/M-type plasmid isolated from a Klebsiella pneumoniae strain from France. Moreover, we report the transfer of a 60-kb OXA-48-encoding plasmid from Klebsiella pneumoniae to other Enterobacteriaceae in two patients.

Cardiac device-related endocarditis caused by Paenibacillus glucanolyticus.

We report the first case of Paenibacillus glucanolyticus infection in a 65-year-old patient with type 2 diabetes who developed a cardiac device-related endocarditis. The identification of the isolate was performed using phenotypic methods, including mass spectrometry-based methods, and 16S rRNA gene sequencing.

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.

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.

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.