Identification of Staphylococcus saprophyticus isolated from patients with urinary tract infection using a simple set of biochemical tests correlating with 16S-23S interspace region molecular weight patterns

Whole genome sequence analysis of multi-drug resistant and biofilm-forming Staphylococcus haemolyticus isolated from bovine milk

BACKGROUND

Milk is an excellent growth medium for microorganisms due to its nutritive composition. Microorganisms have been implicated in bovine mastitis (BM) in dairy cows as well as causing infections in animals and humans. Despite extensive endeavours to manage BM, this condition continues to persist as the most prevalent and economically burdensome problem affecting dairy cattle on a global scale. Non-aureus staphylococci (NAS) species such as Staphylococcus haemolyticus, S. epidermidis, and S. xylosus are currently the predominant microbiological agents identified as the main cause of subclinical udder infections and are also considered opportunistic pathogens in cases of clinical mastitis in dairy cows. Therefore, it is crucial to elucidate the genetic profile of these species. The primary objective of this study was to characterise three phenotypically determined multidrug-resistant NAS environmental strains (NWU MKU1, NWU MKU2, and NWU MKS3) obtained from dairy cows milk via whole-genome sequencing.

RESULTS

The results confirmed that the three isolates were S. haemolyticus with genome sizes of 2.44, 2.56, and 2.56 Mb and a G + C content of 32.8%. The genomes contained an array of antibiotic resistance genes that may potentially confer resistance to a range of antibiotic classes, such as macrolides, fluoroquinolones, aminoglycosides, cephalosporins, tetracyclines, peptides, and phenicol. Furthermore, all the genomes carried virulence genes, which are responsible for several functions, such as adhesion, enzyme and toxin production. The genomes of these organisms contained signatures encoding mobile genetic elements such as prophages and insertion sequences.

CONCLUSION

These findings indicate there is a need for diligent monitoring with improved management practices and quality control strategies on farms to safeguard milk production systems and human health.

Highly efficient enrichment and identification of pathogens using a herringbone microfluidic chip and by MALDI-TOF mass spectrometry

Bacterial infections cause considerable morbidity and expensive healthcare costs. The prescription of broad-spectrum antimicrobial drugs results in failure of treatment or overtreatment and exacerbates the spread of multidrug-resistant pathogens. There is an emergent demand for rapid and accurate methods to identify pathogens and conduct personalized therapy. Here, we develop a herringbone microfluidic chip integrated with vancomycin modified magnetic beads (herringbone-VMB microchip) to enrich pathogens. The enriched pathogens are identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The herringbone-VMB microchip applies passive mixing of bacterial samples by generating microvortices, which significantly enhances the interaction between bacteria and vancomycin modified magnetic beads and leads to more efficient enrichment compared to in-tube extraction. Four common pathogens in urinary tract infections are utilized to validate the method, and the capture efficiency of the bacteria from urine is up to 90%. The whole procedure takes 1.5 hours from enrichment to identification. This method shows potential in shortening the turnaround time in the clinical diagnosis of bacterial infections.

Production, purification and biochemical characterisation of a novel lipase from a newly identified lipolytic bacterium Staphylococcus caprae NCU S6

A novel lipase, SCNL, was isolated from Staphylococcus caprae NCU S6 strain in the study. The lipase was purified to homogeneity with a yield of 6.13% and specific activity of 502.76 U/mg, and its molecular weight was determined to be approximately 87 kDa. SCNL maintained above 80% of its initial activity at a wide range of temperatures (20-50 °C) and pH values (6-11), with an optimal temperature at 40 °C and optimal pH at 9.0 with p-nitrophenyl palmitate as a substrate. SCNL exhibited a higher residual activity than the other staphylococcal lipases in the presence of common enzyme inhibitors and commercial detergents. The lipase activity was enhanced by organic solvents (isooctane, glycerol, DMSO and methanol) and metal ions (Na⁺, Ba²⁺, Ca²⁺, and Mn²⁺). The Km and Vmax values of SCNL were 0.695 mM and 262.66 s^-1mM^-1, respectively. The enzyme showed a preference for p-NP stearate, tributyrin and canola oil. These biochemical features of SCNL suggested that it may be an excellent novel lipase candidate for industrial and biotechnological applications.

A Rapid Assay to Assess Nitrification Inhibition Using a Panel of Bacterial Strains and Partial Least Squares Modeling

As a proof of concept, a rapid assay consisting of a cell-based biosensor (CBB) panel of pure bacterial strains, a fluorescent dye, and partial least squares (PLS) modeling was developed to assess the nitrification inhibition potential of industrial wastewater (WW) samples. The current standard method used to assess the nitrification inhibition potential is the specific nitrification rate (SNR) batch test, which requires approximately 4 h to complete under the watch of an experienced operator. In this study, we exposed the CBB panel of seven bacterial strains (nitrifying and non-nitrifying) to 28 different industrial WW samples and then probed both the membrane integrity and cellular activity using a commercially available "live/dead" fluorescent dye. The CBB panel response acts as a surrogate measurement for the performance of nitrification. Of the seven strains, four (Nitrospira, Escherichia coli, Bacillus subtilis, Bacillus cereus) were identified via the modeling technique to be the most significant contributors for predicting the nitrification inhibition potential. The key outcome from this work is that the CBB panel fluorescence data (collected in approximately 10 min) can accurately predict the outcome of an SNR batch test (that takes 4 h) when performed with the same WW samples and has a strong potential to approximate the chemical composition of these WW samples using PLS modeling. Overall, this is a powerful technique that can be used for point-of-use detection of nitrification inhibition.

Atypical organic-solvent tolerant bacterial hormone sensitive lipase-like homologue EstAG1 from Staphylococcus saprophyticus AG1: Synthesis and characterization

Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Some of the most industrially relevant enzymes of this type are lipolytic and their market is predicted to uphold leadership up till 2024. In this study, a novel bacterial hormone-sensitive lipase-like (bHSL) family homologue, designated EstAG1, was discovered by mining gDNA of bacteria isolated from fat contaminated soil in Lithuania. Putative lipolytic enzyme was cloned, overexpressed in E. coli, purified and characterized determining its biochemical properties. While the true physiological role of the discovered leaderless, ~36 kDa enzyme is unknown, metal-activated EstAG1 possessed optima at 45-47.5 °C, pH 7.5-8, with a generally intermediate activity profile between esterases and lipases. Furthermore, EstAG1 was hyperactivated by ethanol, dioxane and DMSO, implicating that it could be industrially applicable enzyme for the synthesis of valuable products such as biodiesel, flavor esters, etc. Sequence analysis and structure modeling revealed that the highest sequence homology of EstAG1 with the closest structurally and functionally described protein makes up only 26%. It was also revealed that EstAG1 has some differences in the bHSL family-characteristic conserved sequence motives. Therefore, EstAG1 presents interest both in terms of biotechnological applications and basic research.

Evaluation of MALDI-TOF VITEK®MS and VITEK® 2 system for the identification of Staphylococcus saprophyticus

AIM

To compare two identification methods for coagulase-negative staphylococci (CoNS) isolated from patients with urinary tract infections, VITEK^® 2 and MALDI-TOF VITEK^®MS, with genotypic identification by internal transcribed spacer PCR (ITS-PCR).

RESULTS

A total of 217 CoNS isolates were studied. Agreement of the VITEK^® 2 system with ITS-PCR was 84.8%, with 98% sensitivity and 100% specificity. Thirty-one of the 33 strains incorrectly identified by VITEK^® 2 belonged to the species Staphylococcus saprophyticus. MALDI-TOF VITEK^®MS showed an excellent correlation with ITS-PCR since it correctly identified all CoNS isolates.

CONCLUSION

MALDI-TOF VITEK^®MS is more accurate than the automated VITEK^® 2 system in identifying CoNS isolated from urinary tract infections to species level, particularly urinary isolates of S. saprophyticus.

Reprint of "Identification of staphylococcal species based on variations in protein sequences (mass spectrometry) and DNA sequence (sodA microarray)"

This report is among the first using sequence variation in newly discovered protein markers for staphylococcal (or indeed any other bacterial) speciation. Variation, at the DNA sequence level, in the sodA gene (commonly used for staphylococcal speciation) provided excellent correlation. Relatedness among strains was also assessed using protein profiling using microcapillary electrophoresis and pulsed field electrophoresis. A total of 64 strains were analyzed including reference strains representing the 11 staphylococcal species most commonly isolated from man (Staphylococcus aureus and 10 coagulase negative species [CoNS]). Matrix assisted time of flight ionization/ionization mass spectrometry (MALDI TOF MS) and liquid chromatography-electrospray ionization tandem mass spectrometry (LC ESI MS/MS) were used for peptide analysis of proteins isolated from gel bands. Comparison of experimental spectra of unknowns versus spectra of peptides derived from reference strains allowed bacterial identification after MALDI TOF MS analysis. After LC-MS/MS analysis of gel bands bacterial speciation was performed by comparing experimental spectra versus virtual spectra using the software X!Tandem. Finally LC-MS/MS was performed on whole proteomes and data analysis also employing X!tandem. Aconitate hydratase and oxoglutarate dehydrogenase served as marker proteins on focused analysis after gel separation. Alternatively on full proteomics analysis elongation factor Tu generally provided the highest confidence in staphylococcal speciation.

Identification of staphylococcal species based on variations in protein sequences (mass spectrometry) and DNA sequence (sodA microarray)

This report is among the first using sequence variation in newly discovered protein markers for staphylococcal (or indeed any other bacterial) speciation. Variation, at the DNA sequence level, in the sodA gene (commonly used for staphylococcal speciation) provided excellent correlation. Relatedness among strains was also assessed using protein profiling using microcapillary electrophoresis and pulsed field electrophoresis. A total of 64 strains were analyzed including reference strains representing the 11 staphylococcal species most commonly isolated from man (Staphylococcus aureus and 10 coagulase negative species [CoNS]). Matrix assisted time of flight ionization/ionization mass spectrometry (MALDI TOF MS) and liquid chromatography-electrospray ionization tandem mass spectrometry (LC ESI MS/MS) were used for peptide analysis of proteins isolated from gel bands. Comparison of experimental spectra of unknowns versus spectra of peptides derived from reference strains allowed bacterial identification after MALDI TOF MS analysis. After LC-MS/MS analysis of gel bands bacterial speciation was performed by comparing experimental spectra versus virtual spectra using the software X!Tandem. Finally LC-MS/MS was performed on whole proteomes and data analysis also employing X!tandem. Aconitate hydratase and oxoglutarate dehydrogenase served as marker proteins on focused analysis after gel separation. Alternatively on full proteomics analysis elongation factor Tu generally provided the highest confidence in staphylococcal speciation.