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

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.

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.

Evaluating the antibacterial efficacy of a silver nanocomposite surface coating against nosocomial pathogens as an antibiofilm strategy to prevent hospital infections

Antimicrobial nanocoatings may be a means of preventing nosocomial infections, which account for significant morbidity and mortality. The role of hospital sink traps in these infections is also increasingly appreciated. We describe the preparation, material characterization and antibacterial activity of a pipe cement-based silver nanocoating applied to unplasticized polyvinyl chloride, a material widely used in wastewater plumbing. Three-dimensional surface topography imaging and scanning electron microscopy showed increased roughness in all surface finishes versus control, with grinding producing the roughest surfaces. Silver stability within nanocoatings was >99.89% in deionized water and bacteriological media seeded with bacteria. The nanocoating exhibited potent antibiofilm (99.82-100% inhibition) and antiplanktonic (99.59-99.99% killing) activity against three representative bacterial species and a microbial community recovered from hospital sink traps. Hospital sink trap microbiota were characterized by sequencing the 16S rRNA gene, revealing the presence of opportunistic pathogens from genera including Pseudomonas, Enterobacter and Clostridioides. In a benchtop model sink trap system, nanocoating antibiofilm activity against this community remained significant after 11 days but waned following 25 days. Silver nanocoated disks in real-world sink traps in two university buildings had a limited antibiofilm effect, even though in vitro experiments using microbial communities recovered from the same traps demonstrated that the nanocoating was effective, reducing biofilm formation by >99.6% and killing >98% of planktonic bacteria. We propose that conditioning films forming in the complex conditions of real-world sink traps negatively impact nanocoating performance, which may have wider relevance to development of antimicrobial nanocoatings that are not tested in the real-world.

Screening of heavy metal-resistant rhizobial and non-rhizobial microflora isolated from Trifolium sp. growing in mining areas

Plant growth-promoting rhizobacteria (PGPR) can promote plant growth and development with several beneficial effects, especially in challenging environmental conditions, such as the presence of toxic contaminants. In this study, 49 isolates obtained from Trifolium sp. nodules growing on a Pb/Zn mine site were characterized for PGP traits including siderophores production, phosphate solubilization, extracellular enzymes production, and antifungal activity. The isolates were also screened for their ability to grow at increasing concentrations of NaCl and heavy metals, including lead, zinc, cobalt, copper, nickel, cadmium, and chromium. The findings of our study indicated that isolates Cupriavidus paucula RSCup01-RSCup08, Providencia rettgeri RSPro01, Pseudomonas putida RSPs01, Pseudomonas thivervalensis RSPs03-RSPs09, and Acinetobacter beijerinckii RSAci01 showed several key traits crucial for promoting plant growth, thus demonstrating the greatest potential. Most isolates displayed resistance to salt and heavy metals. Notably, Staphylococcus xylosus RSSta01, Pseudomonas sp. RSPs02, Micrococcus yunnanensis RSMicc01, and Kocuria dechangensis RSKoc01 demonstrated a significant capacity to grow at salt concentrations ranging from 10 to 20%, and isolates including Cupravidus paucula RSCup01-RSCup08 exhibited resistance to high levels of heavy metals, up to 1300 mg/L Pb++, 1200 mg/L Zn++, 1000 mg/L Ni++, 1000 mg/L Cd++, 500 mg/L Cu++, 400 mg/L Co++, and 50 mg/L CrVI+. Additionally, the analysis revealed that metal-resistant genes pbrA, czcD, and nccA were exclusively detected in the Cupriavidus paucula RSCup01 strain. The results of this study provide insights into the potential of plant growth-promoting rhizobacteria strains that might be used as inoculants to improve phytoremediation in heavy metal-contaminated soils.

The Urinary Metabolome of Newborns with Perinatal Complications

Maternal pathological conditions such as infections and chronic diseases, along with unexpected events during labor, can lead to life-threatening perinatal outcomes. These outcomes can have irreversible consequences throughout an individual's entire life. Urinary metabolomics can provide valuable insights into early physiological adaptations in healthy newborns, as well as metabolic disturbances in premature infants or infants with birth complications. In the present study, we measured 180 metabolites and metabolite ratios in the urine of 13 healthy (hospital-discharged) and 38 critically ill newborns (admitted to the neonatal intensive care unit (NICU)). We used an in-house-developed targeted tandem mass spectrometry (MS/MS)-based metabolomic assay (TMIC Mega) combining liquid chromatography (LC-MS/MS) and flow injection analysis (FIA-MS/MS) to quantitatively analyze up to 26 classes of compounds. Average urinary concentrations (and ranges) for 167 different metabolites from 38 critically ill NICU newborns during their first 24 h of life were determined. Similar sets of urinary values were determined for the 13 healthy newborns. These reference data have been uploaded to the Human Metabolome Database. Urinary concentrations and ranges of 37 metabolites are reported for the first time for newborns. Significant differences were found in the urinary levels of 44 metabolites between healthy newborns and those admitted at the NICU. Metabolites such as acylcarnitines, amino acids and derivatives, biogenic amines, sugars, and organic acids are dysregulated in newborns with bronchopulmonary dysplasia (BPD), asphyxia, or newborns exposed to SARS-CoV-2 during the intrauterine period. Urine can serve as a valuable source of information for understanding metabolic alterations associated with life-threatening perinatal outcomes.

Bacterial contamination of water used as thermal transfer fluid in fluid-warming devices

INTRODUCTION

Recent reports implicated heater-cooler units (HCUs), which are used for warming infusions, blood or in extracorporeal membrane oxygenation devices, as a possible origin of healthcare-associated infections (HAIs) with potentially pathogenic bacteria, such as non-tuberculous mycobacteria [1]. This represents a source of contamination in a usually sterile setting.

AIM

To analyse water from infusion heating devices (IHDs) for bacterial contamination, and to determine if IHDs are a potential source in the transmission of HAIs.

METHODS

Thermal transfer fluid (TTF; 300-500 mL) was collected from the reservoirs of 22 independent IHDs and processed on different selective and non-selective media for colony count and identification of bacteria. Strains of Mycobacterium spp. were analysed by whole-genome sequencing.

RESULTS

Bacterial growth was observed in all 22 TTF samples after cultivation at 22 °C and 36 °C. Pseudomonas aeruginosa was the most frequent pathogen identified, present in 13.64% (3/22) of samples at >100 colony-forming units/100 mL. Colonization with Mycobacterium chimaera, Ralstonia pickettii and Ralstonia mannitolilytica was detectable in 9.09% (2/22) of samples. Primary sequencing of the detected M. chimaera suggests a close relationship with a M. chimaera strain detected in an outbreak in Switzerland which led to the death of two patients.

DISCUSSION

Contamination of TTF represents a germ reservoir in a sensitive setting. Handling errors of IHDs may lead to the distribution of opportunistic or facultative bacterial pathogens, increasing the risk of transmission of nosocomial infections.

Complete bacterial profile and potential pathogens of cat fleas Ctenocephalides felis

Fleas are important ectoparasites and vectors associated with a wide range of pathogenic diseases, posing threats to public health concerns, especially cat fleas that spread worldwide. Understanding the microbial components is essential due to cat fleas are capable of transmitting pathogens to humans, causing diseases like plague and murine typhus. In the present study, metagenomic next-generation sequencing was applied to obtain the complete microbiota and related functions in the gut of Ctenocephalides felis. A total of 1,870 species was taxonomically recognized including 1,407 bacteria, 365 eukaryotes, 69 viruses, and 29 archaea. Proteobacteria was the dominant phylum among the six samples. Pathogens Rickettsia felis, Acinetobacter baumannii, Coxiella burnetii, and Anaplasma phagocytophilum were taxonomically identified and had high abundances in all samples. The resistance gene MexD was predominant in microbial communities of all cat fleas. We also performed epidemiological surveys of pathogens R. felis, A. baumannii, C. burnetii, and A. phagocytophilum among 165 cat fleas collected from seven provinces in China, while only the DNAs of R. felis (38/165, 23.03%) and C. burnetii (2/165, 1.21%) were obtained. The data provide new insight and understanding of flea intestinal microbiota and provided novel information for preventing and controlling fleas and their transmitted diseases.