In vitro activity of 20 antibiotics against Cupriavidus clinical strains

A new nodule-associated bacterium, Cupriavidus consociatus sp. nov. Isolated from the root nodules of Leucaena sp. and Arachis sp. growing in a cacao field in Chiapas, Mexico

Cupriavidus is a genus of bacteria that inhabit diverse ecological niches, including plant-associated and nodulating species. A previous survey of legume plants in the south of Mexico resulted in the isolation of several bacteria. This present study describes two Cupriavidus strains isolated from the nodules of Leucaena sp. and Arachis sp. plants growing in a cacao field in Chiapas, Mexico. Both strains (LEh25T and LEh21) shared identical 16S rRNA gene sequences and 98.4% identity with Cupriavidus oxalaticus Ox1T. However, the in silico average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values (99.99 and 99.90% similarity, respectively) indicated that they belonged to different genomic species when compared to type strains of Cupriavidus species (ANI ~ 93.2 and dDDH ~ 50% similarity). Phylogenomic analysis indicated that the novel species would be placed in the genus Cupriavidus next to C. oxalaticus Ox1T. Neither strain could fix nitrogen in a semisolid medium, and the interactions of the type strain with Phaseolus vulgaris, and Leucaena sp. revealed the formation of nodules, although these were ineffective. The genomic analysis demonstrated the presence of nitrogen fixation and nodulation genes with the same organization as in other strains of Cupriavidus and Paraburkholderia, although lacking NodB. To complement the study of the novel species, the strains were phenotypically and chemotaxonomically analyzed, with the results indicating differences with C. oxalaticus Ox1T and other similar type strains of Cupriavidus species. From these results, we propose the novel species Cupriavidus consociatus sp. nov. with the type strain LEh25T=TSD-314T = CDBB B-2085T.

Antibiotic resistance patterns and cross-family ARG transfer in families Burkholderiaceae and Sphingomonadaceae: A large-scale genome-wide analysis of over 10 K genomes

Members of Burkholderiaceae and Sphingomonadaceae play an active role in pollutant degradation, yet their antibiotic resistance risks are frequently overlooked. This study analyzed 9406 Burkholderiaceae and 2343 Sphingomonadaceae genomes to investigate the distribution, horizontal gene transfer (HGT), and co-occurrence patterns of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs). ARGs were prevalent in Burkholderiaceae (93.2 % of genomes), dominated by bacitracin (89.0 %), multidrug (88.1 %), and beta-lactam (40.5 %) resistance, while Sphingomonadaceae exhibited lower ARG prevalence (11.6 %). Notably, Burkholderia and Caballeronia displayed high multidrug resistance (10.1 ARGs per genome) and frequent ARG-MRG co-occurrence (84.4 %). Strong ARG-MRG-MGE correlations were observed in Burkholderiaceae, suggesting MGEs play a key role in resistance dissemination. Additionally, ARGs correlated with metabolic genes, linking metabolic versatility to resistance. Genes like capO (chloramphenicol oxidase) and blaTEM-116 (beta-lactamase) were shared among distantly related genera, while mcr-5.1 (MCR phosphoethanolamine transferase) co-occurred with MRGs across Cupriavidus species, highlighting HGT and co-selection risks. ARG transfer between Burkholderiaceae, Sphingomonadaceae and clinical pathogens was frequent (114-1306 events/10,000 genome pairs), with sulfonamide resistance dominating (51.3 % of HGT). These findings highlight Burkholderiaceae and Sphingomonadaceae as critical reservoirs of resistance genes and emphasize the need for enhanced surveillance and mitigation strategies to curb the spread of multidrug resistance.

Genomic insights and phenotypic characterization of three multidrug resistant Cupriavidus strains from the cystic fibrosis lung

AIMS

We aimed to investigate phenotypic and genomic traits of three Cupriavidus spp. isolates recovered from people with cystic fibrosis (PWCF). These bacteria are recognized as emerging pathogens in PWCF.

METHODS AND RESULTS

Using short and long sequencing reads, we assembled three hybrid complete genomes for the genus Cupriavidus, adding to the 45 published currently, describing multipartite genomes and plasmids. The isolates likely represent three different species, and they carry a cumulative total of 30 antibiotic resistance genes with high homology to well-characterized resistance determinants from other bacteria. Multidrug resistance to antibiotics used in CF management was observed in all three isolates. However, two treatments were active across all isolates: cefotaxime and piperacillin/tazobactam. Biofilm formation was only seen at physiological temperatures (37°C) and lost at 20°C and all isolates had low lethality in Galleria mellonella larvae. Isolates demonstrated variable motility, with one non-motile isolate carrying a disrupted flhD transcriptional regulator, abolishing flagella expression.

CONCLUSIONS

Our Cupriavidus spp. isolates showed considerable genomic and phenotypic variability that may impact their virulence and treatment in PWCF, where multidrug resistance will negate treatments and biofilm formation and motility play key roles in infection establishment, as seen in CF pathogens like Pseudomonas aeruginosa. More detailed investigation of clinical Cupriavidus isolates is needed for full understanding of the risk they pose to PWCF.

Cupriavidus pauculus Infection Associated With Extracorporeal Membrane Oxygenation in a Pediatric Patient

We describe a critically ill neonate in the postoperative period of complex cardiovascular surgery who required extracorporeal membrane oxygenation (ECMO) and developed bacteremia caused by Cupriavidus pauculus. This uncommon infection in pediatric patients associated with ECMO highlights the diagnostic suspicion of bacteremia due to this non-fermentative Gram-negative bacillus. The report emphasizes early clinical evaluation and treatment and underscores the need for strict protocols to disinfect ECMO circuits, alerting health institutions to the potential transmission risk through these systems.

Resistance to carbapenems in the urban soil isolate Cupriavidus taiwanensis S2-1-W is associated with OXA-1206, a newly discovered carbapenemase

AIMS

Cupriavidus isolates are found in environmental and clinical samples and are often resistant to carbapenems, which are last-resort antibiotics. However, their carbapenem-resistance molecular mechanisms remain unknown. This study aimed to (i) characterize and sequence the carbapenem-resistant soil isolate Cupriavidus taiwanensis S2-1-W to uncover its antibiotic resistance determinants; and (ii) clone and characterize a putative novel carbapenemase gene identified in this isolate.

METHODS AND RESULTS

Antibiotic susceptibility testing of C. taiwanensis S2-1-W revealed that it was resistant to most carbapenems, other β-lactams, and aminoglycosides tested. Genome sequencing of this isolate revealed a complex chromosomal resistome that included multidrug efflux pump genes, one aminoglycoside transferase gene, and three β-lactamase genes. Among them, we identified a novel putative class D β-lactamase gene (blaOXA-1206) that is highly conserved among other sequenced C. taiwanensis isolates. Cloning and characterization of blaOXA-1206 confirmed that it encodes for a newly discovered carbapenemase (OXA-1206) that confers resistance to carbapenems and other β-lactams.

CONCLUSION

Carbapenem-resistance in C. taiwanensis S2-1-W is associated with a newly discovered carbapenemase, OXA-1206.

Genomic Sequencing of Clinical Cupriavidus gilardii Isolates Revealed Their Diverse Antimicrobial Resistance Mechanisms

Purpose

Cupriavidus gilardii is an emerging multidrug-resistant pathogen found in many environments and few clinical samples. The clinical infectiousness, pathogenicity, and resistance mechanisms of C. gilardii are still unclear due to the lack of clinical and sequencing data. We need to obtain insight into the clinical characteristics, virulence, and resistance mechanisms of C. gilardii.

Patients and Methods

We isolated five C. gilardii isolates from hospitalized patients and carried out assay, culture and genome sequencing. We analyzed the genomic features of clinical C. gilardii isolates and took insight into their clinical characteristics, virulence, and resistance mechanisms.

Results

These isolates were resistant to meropenem, gentamicin, and other antimicrobials due to intrinsic resistance genes. Furthermore, the sequencing results revealed the widespread presence of the MCR-5.1 gene in C. gilardii. The virulence magnitude of C. gilardii is closely correlated with the number of virulence factors they carry. Some C. gilardii strains can acquire resistance to levofloxacin through gyrA gene mutation during treatment. The diverse antimicrobial resistance mechanisms challenge the treatment of C. gilardii infections.

Conclusion

We present the genomic characteristics of clinically isolated C. gilardii to improve (i) our understanding of this pathogen and (ii) treatment options.

MALDI-TOF MS analysis of Burkholderia pseudomallei and closely related species isolated from soils and water in Khon Kaen, Thailand

Melioidosis is caused by Burkholderia pseudomallei (Bp) acquired from the environment. Conventional identification methods for environmental Bp are challenging due to the presence of closely related species. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is accurate for bacterial identification, but has been little used to identify Bp from environmental samples. This study aims to evaluate MALDI-TOF MS for the identification of Bp and closely related species isolated from environmental samples in Thailand using whole-genome sequencing (WGS) as the gold standard, including determining the best sample preparation method for this purpose. We identified Bp (n = 22), Burkholderia spp. (n = 28), and other bacterial species (n = 32) using WGS. MALDI-TOF analysis of all Bp isolates yielded results consistent with WGS. A decision-tree algorithm identified 16 important variable peaks, using the protein extraction method (PEM), demonstrating distinct MALDI-TOF profiles for the three categories (Bp, Burkholderia spp. and "other bacterial species"). Three biomarker peaks (4060, 5196, and 6553 Da) could discriminate Bp from other Burkholderia and closely related species with 100% sensitivity and specificity. Hence, the MALDI-TOF technique has shown its potential as a species discriminatory tool, providing results comparable to WGS for classification and surveillance of environmental Bp.

First Case of Cupravidus paculus Infection in a Lung Transplant Recipient: A Case Report

Cupravidus paculus is a rare Gram-negative bacterium that can cause a wide range of severe infections, largely in immunocompromised patients. It is a ubiquitous organism found in natural and man-made environments and in the hospital. Herein, we present the first case of C. paculus infection in a lung transplant recipient, which required prolonged antibiotic therapy to achieve complete clearance. Additionally, we review the existing literature on the clinical and microbiological profile of C. paculus, along with previously documented cases of clinical infections. Our case highlights the potential sources of C. paculus infections, the importance of appropriate disinfection protocols for medical devices, and the need for antibiotic sensitivities to guide treatment.

Infection caused by Cupriavidus gilardii in a convalescent COVID-19 patient

Cupriavidus gilardii is an aerobic, gram-negative bacillus that can opportunistically infect immunocompromised patients or those undergoing invasive procedures. We reported a case caused by C. gilardii in a previously basic healthy 78-year-old male, who had COVID-19 and had used corticosteroids recently. The bacterium was identified as C. gilardii by the metagenomic next-generation sequencing from the patient's bronchoalveolar lavage fluid and blood. In addition, this is the first time that we isolated C. gilardii from bronchoalveolar lavage fluid, which provides clinical experience in rare bacterial infections.

Wholegrain fermentation affects gut microbiota composition, phenolic acid metabolism and pancreatic beta cell function in a rodent model of type 2 diabetes

The intestinal microbiota plays an important role in host metabolism via production of dietary metabolites. Microbiota imbalances are linked to type 2 diabetes (T2D), but dietary modification of the microbiota may promote glycemic control. Using a rodent model of T2D and an in vitro gut model system, this study investigated whether differences in gut microbiota between control mice and mice fed a high-fat, high-fructose (HFHFr) diet influenced the production of phenolic acid metabolites following fermentation of wholegrain (WW) and control wheat (CW). In addition, the study assessed whether changes in metabolite profiles affected pancreatic beta cell function. Fecal samples from control or HFHFr-fed mice were fermented in vitro with 0.1% (w/v) WW or CW for 0, 6, and 24 h. Microbiota composition was determined by bacterial 16S rRNA sequencing and phenolic acid (PA) profiles by UPLC-MS/MS. Cell viability, apoptosis and insulin release from pancreatic MIN6 beta cells and primary mouse islets were assessed in response to fermentation supernatants and selected PAs. HFHFr mice exhibited an overall dysbiotic microbiota with an increase in abundance of proteobacterial taxa (particularly Oxalobacteraceae) and Lachnospiraceae, and a decrease in Lactobacillus. A trend toward restoration of diversity and compositional reorganization was observed following WW fermentation at 6 h, although after 24 h, the HFHFr microbiota was monodominated by Cupriavidus. In parallel, the PA profile was significantly altered in the HFHFr group compared to controls with decreased levels of 3-OH-benzoic acid, 4-OH-benzoic acid, isoferulic acid and ferulic acid at 6 h of WW fermentation. In pancreatic beta cells, exposure to pre-fermentation supernatants led to inhibition of insulin release, which was reversed over fermentation time. We conclude that HFHFr mice as a model of T2D are characterized by a dysbiotic microbiota, which is modulated by the in vitro fermentation of WW. The differences in microbiota composition have implications for PA profile dynamics and for the secretory capacity of pancreatic beta cells.

Bioremediation of copper in sediments from a constructed wetland ex situ with the novel bacterium Cupriavidus basilensis SRS

The H-02 constructed wetland was designed to remove metals (primarily copper and zinc) to treat building process water and storm water runoff from multiple sources associated with the Tritium Facility at the DOE-Savannah River Site, Aiken, SC. The concentration of Cu and Zn in the sediments has increased over the lifetime of the wetland and is a concern. A bioremediation option was investigated at the laboratory scale utilizing a newly isolated bacterium of the copper metabolizing genus Cupriavidus isolated from Tim's Branch Creek, a second-order stream that eventually serves as a tributary to the Savannah River, contaminated with uranium and other metals including copper, nickel, and mercury. Cupriavidus basilensis SRS is a rod-shaped, gram-negative bacterium which has been shown to have predatory tendencies. The isolate displayed resistance to the antibiotics ofloxacin, tetracycline, ciprofloxacin, select fungi, as well as Cu²⁺ and Zn²⁺. Subsequent ribosomal sequencing demonstrated a 100% confidence for placement in the genus Cupriavidus and a 99.014% match to the C. basilensis type strain. When H-02 wetland samples were inoculated with Cupriavidus basilensis SRS samples showed significant (p < 0.05) decrease in Cu²⁺ concentrations and variability in Zn²⁺ concentrations. Over the 72-h incubation there were no significant changes in the inoculate densities (10⁶-10⁸ cells/ML) indicating Cupriavidus basilensis SRS resiliency in this environment. This research expands our understanding of the Cupriavidus genus and demonstrates the potential for Cupriavidus basilensis SRS to bioremediate sites impacted with heavy metals, most notably copper.

Lab-Scale Cultivation of Cupriavidus necator on Explosive Gas Mixtures: Carbon Dioxide Fixation into Polyhydroxybutyrate

Aerobic, hydrogen oxidizing bacteria are capable of efficient, non-phototrophic CO2 assimilation, using H2 as a reducing agent. The presence of explosive gas mixtures requires strict safety measures for bioreactor and process design. Here, we report a simplified, reproducible, and safe cultivation method to produce Cupriavidus necator H16 on a gram scale. Conditions for long-term strain maintenance and mineral media composition were optimized. Cultivations on the gaseous substrates H2, O2, and CO2 were accomplished in an explosion-proof bioreactor situated in a strong, grounded fume hood. Cells grew under O2 control and H2 and CO2 excess. The starting gas mixture was H2:CO2:O2 in a ratio of 85:10:2 (partial pressure of O2 0.02 atm). Dissolved oxygen was measured online and was kept below 1.6 mg/L by a stepwise increase of the O2 supply. Use of gas compositions within the explosion limits of oxyhydrogen facilitated production of 13.1 ± 0.4 g/L total biomass (gram cell dry mass) with a content of 79 ± 2% poly-(R)-3-hydroxybutyrate in a simple cultivation set-up with dissolved oxygen as the single controlled parameter. Approximately 98% of the obtained PHB was formed from CO2.

Cupriavidus spp and other waterborne organisms in healthcare water systems across the United Kingdom

BACKGROUND

Cupriavidus pauculus is a rare clinical pathogen with cases having been linked to contaminated hospital water systems. An outbreak of three cases of C. pauculus and other waterborne organisms was reported in a Glasgow hospital in 2018.

AIMS

The aim of this study was to determine whether Cupriavidus spp are present in hospital water systems elsewhere in Scotland and the UK and to ascertain the optimal laboratory methodology for detection. We also sought to establish where in the water system these organisms are detected and whether a selective media could be developed for isolation. In addition, we tested water samples for the presence of other Gram negative waterborne organisms.

METHODS

Water samples were received from ten UK NHS hospitals and from various parts of the water system. Isolates were plated on to TSA and Pseudomonas Isolation Agar and further identified using MALDI-TOF and 16S PCR FINDINGS: Cupriavidus spp. were detected in four of ten hospitals tested and all five isolates were from the periphery of the water system. All hospitals had evidence of other OPPPs. Cupriavidus spp. were identified using TSA, with some isolates growing on Pseudomonas isolation agar; as such they may be inadvertently be detected when testing water specifically for Pseudomonas aeruginosa.

CONCLUSION

This study demonstrates that isolation of Cupriavidus spp. was not unique to the Glasgow incident, these bacteria being present in hospital water systems elsewhere in the UK. We therefore recommend water testing in response to clinical cases. Consideration should also be given to water testing following bacteraemias due to other rare and unusual water borne pathogens.

Hospital sink traps as a potential source of the emerging multidrug-resistant pathogen Cupriavidus pauculus: characterization and draft genome sequence of strain MF1

Introduction.Cupriavidus pauculus is historically found in soil and water but has more recently been reported to cause human infection and death. Hospital sink traps can serve as a niche for bacterial persistence and a platform for horizontal gene transfer, with evidence of dissemination of pathogens in hospital plumbing systems driving nosocomial infection.

Gap Statement. This paper presents the first C. pauculus strain isolated from a hospital sink trap. There are only six genome assemblies available on NCBI for C. pauculus; two of these are PacBio/Illumina hybrids. This paper presents the first ONT/Illumina hybrid assembly, with five contigs. The other assemblies available consist of 37, 38, 111 and 227 contigs. This paper also presents data on biofilm formation and lethal dose in Galleria mellonella; there is little published information describing these aspects of virulence.

Aim. The aims were to identify the isolate found in a hospital sink trap, characterize its genome, and assess whether it could pose a risk to human health.

Methodology. The genome was sequenced, and a hybrid assembly of short and long reads produced. Antimicrobial susceptibility was determined by the broth microdilution method. Virulence was assessed by measuring in vitro biofilm formation compared to Pseudomonas aeruginosa and in vivo lethality in Galleria mellonella larvae.

Results. The isolate was confirmed to be a strain of C. pauculus, with a 6.8 Mb genome consisting of 6468 coding sequences and an overall G+C content of 63.9 mol%. The genome was found to contain 12 antibiotic resistance genes, 8 virulence factor genes and 33 metal resistance genes. The isolate can be categorized as resistant to meropenem, amoxicillin, amikacin, gentamicin and colistin, but susceptible to cefotaxime, cefepime, imipenem and ciprofloxacin. Clear biofilm formation was seen in all conditions over 72 h and exceeded that of P. aeruginosa when measured at 37 °C in R2A broth. Lethality in G. mellonella larvae over 48 h was relatively low.

Conclusion. The appearance of a multidrug-resistant strain of C. pauculus in a known pathogen reservoir within a clinical setting should be considered concerning. Further work should be completed to compare biofilm formation and in vivo virulence between clinical and environmental strains, to determine how easily environmental strains may establish human infection. Infection control teams and clinicians should be aware of the emerging nature of this pathogen and further work is needed to minimize the impact of contaminated hospital plumbing systems on patient outcomes.

In Vitro Activity of 22 Antibiotics against Achromobacter Isolates from People with Cystic Fibrosis. Are There New Therapeutic Options?

Bacteria belonging to the genus Achromobacter are increasingly isolated from respiratory samples of people with cystic fibrosis (PWCF). The management of this multidrug-resistant genus is challenging and characterised by a lack of international recommendations, therapeutic guidelines and data concerning antibiotic susceptibility, especially concerning the newer antibiotics. The objective of this study was to describe the antibiotic susceptibility of Achromobacter isolates from PWCF, including susceptibility to new antibiotics. The minimum inhibitory concentrations (MICs) of 22 antibiotics were determined for a panel of 23 Achromobacter isolates from 19 respiratory samples of PWCF. Two microdilution MIC plates were used: EUMDROXF^® plate (Sensititre) and Micronaut-S Pseudomonas MIC^® plate (Merlin) and completed by a third method if necessary (E-test^® or UMIC^®). Among usual antimicrobial agents, the most active was imipenem (70% susceptibility). Trimethoprim-sulfamethoxazole, piperacillin and tigecycline (65%, 56% and 52% susceptibility, respectively) were still useful for the treatment of Achromobacter infections. Among new therapeutic options, β-lactams combined with a β-lactamase-inhibitor did not bring benefits compared to β-lactam alone. On the other hand, cefiderocol appeared as a promising therapeutic alternative for managing Achromobacter infections in PWCF. This study provides the first results on the susceptibility of clinical Achromobacter isolates concerning new antibiotics. More microbiological and clinical data are required to establish the optimal treatment of Achromobacter infections.

MCR-5-Producing Colistin-Resistant Cupriavidus gilardii Strain from Well Water in Batna, Algeria

This paper presents the first description of the mcr-5.1 gene in a colistin-resistant Cupriavidus gilardii isolate from well water that supplies a maternity hospital in Algeria. The whole-genome sequence of this strain showed the presence of putative β-lactamase, aac(3)-IVa, and multidrug efflux pump-encoding genes, which could explain the observed multidrug resistance phenotype. Our findings are of great interest, as we highlight a potential contamination route for the spread of mcr genes.

IMPORTANCE Colistin resistance mediated by mcr genes in Gram-negative bacteria has gained significant attention worldwide. This is due to the ability of these genes to be horizontally transferred between different bacterial genera and species. Aquatic environments have been suggested to play an important role in the emergence and spread of this resistance mechanism. Here, we describe the first report of an mcr-5-positive Cupriavidus gilardii aquatic isolate through its isolation from well water in Algeria. The significance of our study is in shedding the light on an important environmental reservoir of mcr genes.