Biofilm characteristics and transcriptomic analysis of Haemophilus parasuis

Identification and Characterization of Non-protein Coding RNA Homologs in Serratia Marcescens by Comparative Transcriptomics

The Serratia marcescens is a Gram-negative bacterium from the Enterobacteriaceae family. Recently, S. marcescens have evolved to become a versatile and opportunistic pathogen. Furthermore, this bacterium is also a multi-drug resistant pathogen exhibiting Extended-Spectrum Beta-Lactamases (ESBL) activity. This bacterium is highly associated with infections in healthcare settings and even leads to death. Hence, an advanced approach based on non-protein coding RNA (npcRNA) of S. marcescens was considered in this study to understand its regulatory roles in virulence, pathogenesis, and the differential expression of these transcripts in various growth phases of the bacterium. BLASTn search of known npcRNAs from Salmonella typhi, Escherichia coli, and Yersinia pestis against S. marcescens was performed to discover putative conserved homologous transcripts. The novelty of these putative homologous npcRNAs was verified by screening through the Rfam web tool. The target mRNA for the homologs was predicted via the TargetRNA2 webtool to understand the possible regulatory roles of these transcripts. The npcRNA homologs, which were predicted to regulate virulence target mRNA were assessed for their expression profile at different growth stages via reverse transcription PCR and the band intensity was quantitatively analysed using the Image J tool. The known npcRNA ssrS, from S. typhi showed expression in S. marcescens during three growth stages (lag, log, and stationary). Expression was observed to be high during the lag phase followed by a similarly low-level expression during the log and no expression during stationary phase. This ssrS homolog was predicted to regulate mRNA that encodes for protein FliR, which is associated with virulence. This is a preliminary study that lay the foundation for further elucidation of more virulence-associated npcRNAs that are yet to be discovered from S. marcescens, which can be useful for diagnostics and therapeutic applications.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01160-y.

Molecular Aspects of the Functioning of Pathogenic Bacteria Biofilm Based on Quorum Sensing (QS) Signal-Response System and Innovative Non-Antibiotic Strategies for Their Elimination

One of the key mechanisms enabling bacterial cells to create biofilms and regulate crucial life functions in a global and highly synchronized way is a bacterial communication system called quorum sensing (QS). QS is a bacterial cell-to-cell communication process that depends on the bacterial population density and is mediated by small signalling molecules called autoinducers (AIs). In bacteria, QS controls the biofilm formation through the global regulation of gene expression involved in the extracellular polymeric matrix (EPS) synthesis, virulence factor production, stress tolerance and metabolic adaptation. Forming biofilm is one of the crucial mechanisms of bacterial antimicrobial resistance (AMR). A common feature of human pathogens is the ability to form biofilm, which poses a serious medical issue due to their high susceptibility to traditional antibiotics. Because QS is associated with virulence and biofilm formation, there is a belief that inhibition of QS activity called quorum quenching (QQ) may provide alternative therapeutic methods for treating microbial infections. This review summarises recent progress in biofilm research, focusing on the mechanisms by which biofilms, especially those formed by pathogenic bacteria, become resistant to antibiotic treatment. Subsequently, a potential alternative approach to QS inhibition highlighting innovative non-antibiotic strategies to control AMR and biofilm formation of pathogenic bacteria has been discussed.

Effect of ferric ions on Cronobacter sakazakii growth, biofilm formation, and swarming motility

Cronobacter sakazakii (C. sakazakii) is a common food-borne pathogen that induces meningitis, sepsis, and necrotizing enterocolitis, primarily in newborns and infants. Iron plays a pivotal role in the growth of cells and biofilm formation. However, the effects of hemin (ferric ion donor) on C. sakazakii cells are scarcely known. Here, we explored the effect of ferric ions on the growth of planktonic C. sakazakii, biofilm formation, and swarming motility by crystal violet staining (CVS), scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and swarming assay. Our study demonstrated that ferric ions facilitated the growth of planktonic C. sakazakii, while hemin at concentrations ranging from 50 to 800 μmol/L promoted biofilm formation and at concentrations between 50 and 200 μmol/L enhanced the swarming motility of C. sakazakii. Furthermore, high hemin concentrations (400-800 μmol/L) were found to reduce flagellar length, as confirmed by transmission electron microscopy (TEM). These findings indicated that ferric ions mediated the swarming motility of C. sakazakii by regulating flagellar assembly. Finally, transcriptomic analysis of C. sakazakii was performed at hemin concentrations of 0, 50, and 200 μmol/L, which revealed that several genes associated with iron transport and metabolism, and flagellar assembly were essential for the survival of C. sakazakii under hemin treatment. Our findings revealed the molecular basis of ferric ions on C. sakazakii growth and biofilm formation, thus providing a novel perspective for its prevention and control.

Drug sensitivity and genome-wide analysis of two strains of Mycoplasma gallisepticum with different biofilm intensity

Mycoplasma gallisepticum (MG) is one of the major causative agents of chronic respiratory diseases in poultry. The biofilms of MG are highly correlated to its chronic infection. However data on genes involved in biofilm formation ability are still scarse. MG strains with distinct biofilm intensity were screened by crystal violet staining morphotyped and characterized for the drug sensitivity. Two MG strains NX-01 and NX-02 showed contrasted ability to biofilm formation. The biofilm formation ability of NX-01 strain was significantly higher than that of NX-02 strain (p < 0.01). The drug sensitivity test showed that the stronger the ability of MG stain to form biofilms, the weaker its sensitivity to 17 antibiotic drugs. Moreover, putative key genes related to biofilm formation were screened by genome-wide analysis. A total of 13 genes and proteins related to biofilm formation, including ManB, oppA, oppD, PDH, eno, RelA, msbA, deoA, gapA, rpoS, Adhesin P1 precursor, S-adenosine methionine synthetase, and methionyl tRNA synthetase were identified. There were five major discrepancies between the two isolated MG strains and the five NCBI-published MG strains. These findings provide potential targets for inhibiting the formation of biofilm of MG, and lay a foundation for treating chronic infection.

Pan-genome wide association study of Glaesserella parasuis highlights genes associated with virulence and biofilm formation

Glaesserella parasuis is a gram-negative bacterium that causes fibrotic polyserositis and arthritis in pig, significantly affecting the pig industry. The pan-genome of G. parasuis is open. As the number of genes increases, the core and accessory genomes may show more pronounced differences. The genes associated with virulence and biofilm formation are also still unclear due to the diversity of G. parasuis. Therefore, we have applied a pan-genome-wide association study (Pan-GWAS) to 121 strains G. parasuis. Our analysis revealed that the core genome consists of 1,133 genes associated with the cytoskeleton, virulence, and basic biological processes. The accessory genome is highly variable and is a major cause of genetic diversity in G. parasuis. Furthermore, two biologically important traits (virulence, biofilm formation) of G. parasuis were studied via pan-GWAS to search for genes associated with the traits. A total of 142 genes were associated with strong virulence traits. By affecting metabolic pathways and capturing the host nutrients, these genes are involved in signal pathways and virulence factors, which are beneficial for bacterial survival and biofilm formation. This research lays the foundation for further studies on virulence and biofilm formation and provides potential new drug and vaccine targets against G. parasuis.

Biofilm characteristics and transcriptomic profiling of Acinetobacter johnsonii defines signatures for planktonic and biofilm cells

Most bacteria in the natural environment have a biofilm mode of life, which is intrinsically tolerant to antibiotics. While until now, the knowledge of biofilm formation by Acinetobacter johnsonii is not well understood. In this study, the characteristics and the effect of a sub-inhibitory concentration of antibiotic on A. johnsonii biofilm and planktonic cells were determined. We discovered a positive relationship between biofilm formation and tetracycline resistance, and biofilms rapidly evolve resistance to tetracycline they are treated with. Persister cells commonly exist in both planktonic and biofilm cells, with a higher frequency in the latter. Further transcriptomic analysis speculates that the overexpression of multidrug resistance genes and stress genes were mainly answered to sub lethal concentration of tetracycline in planktonic cells, and the lower metabolic levels after biofilm formation result in high resistance level of biofilm cells to tetracycline. Altogether, these data suggest that A. johnsonii can adjust its phenotype when grown as biofilm and change its metabolism under antibiotic stress, and provide implications for subsequent biofilm control.

Temporal Patterns of Phenotypic Antimicrobial Resistance and Coinfecting Pathogens in Glaesserella parasuis Strains Isolated from Diseased Swine in Germany from 2006 to 2021

Glaesserella parasuis (Gps) causes high economic losses in pig farms worldwide. So far no vaccine provides cross-protection for different serotypes, so antibiotic treatment is widely used to cope with this pathogen. In this study, routine diagnostic data from 2046 pigs with Gps related diseases sent for necropsy to a German laboratory in the time period 2006–2021 were analysed retrospectively. In the time period 2018–2021, the most frequent serotypes (ST) detected were ST4 (30%) and ST13 (22%). A comparison of the reference period 2006–2013 prior to obligatory routine recording of antimicrobial usage in livestock with the period 2014–2021 resulted in a statistically significant decrease of frequencies of resistant Gps isolates for ceftiofur, enrofloxacin, erythromycin, spectinomycin, tiamulin and tilmicosin. While in 2006–2013 all isolates were resistant for tetracyclin and cephalothin, frequencies of resistant isolates decreased in the second time period to 28% and 62%, respectively. Parallel to the reduction of antimicrobial usage, during recent years a reduction in resistant Gps isolates has been observed, so only a low risk of treatment failure exists. Most frequently, pigs positive for Gps were also positive for S.suis (25.4%), PRRSV-EU (25.1%) and influenza virus (23%). The viral pathogens may act as potential trigger factors.