Spread of R-plasmids among Escherichia coli causing urinary tract infections

Urinary Plasmids Reduce Permissivity to Coliphage Infection

The microbial community of the urinary tract (urinary microbiota or urobiota) has been associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. While urinary Escherichia coli strains associated with urinary tract infection (UTI) and their phages have been catalogued for the urobiome, bacterium-plasmid-phage interactions have yet to be explored. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Putative F plasmids were predicted in 47 of 67 urinary E. coli isolates, and most of these plasmids carried genes that encode toxin-antitoxin (TA) modules, antibiotic resistance, and/or virulence. Urinary E. coli plasmids, from urinary microbiota strains UMB0928 and UMB1284, were conjugated into E. coli K-12 strains. These transconjugants included genes for antibiotic resistance and virulence, and they decreased permissivity to coliphage infection by the laboratory phage P1vir and the urinary phages Greed and Lust. Plasmids in one transconjugant were maintained in E. coli K-12 for up to 10 days in the absence of antibiotic resistance selection; this included the maintenance of the antibiotic resistance phenotype and decreased permissivity to phage. Finally, we discuss how F plasmids present in urinary E. coli strains could play a role in coliphage dynamics and the maintenance of antibiotic resistance in urinary E. coli. IMPORTANCE The urinary tract contains a resident microbial community called the urinary microbiota or urobiota. Evidence exists that it is associated with human health. Bacteriophages (phages) and plasmids present in the urinary tract, like in other niches, may shape urinary bacterial dynamics. Bacterium-plasmid-phage interactions have been studied primarily in laboratory settings and are yet to be thoroughly tested in complex communities. This is especially true of the urinary tract, where the bacterial genetic determinants of phage infection are not well understood. In this study, we characterized urinary E. coli plasmids and their ability to decrease permissivity to E. coli phage (coliphage) infection. Urinary E. coli plasmids, encoding antibiotic resistance and transferred by conjugation into naive laboratory E. coli K-12 strains, decreased permissivity to coliphage infection. We propose a model by which urinary plasmids present in urinary E. coli strains could help to decrease phage infection susceptibility and maintain the antibiotic resistance of urinary E. coli. This has consequences for phage therapy, which could inadvertently select for plasmids that encode antibiotic resistance.

Plasmids of the urinary microbiota

Studies of the last decade have identified a phylogenetically diverse community of bacteria within the urinary tract of individuals with and without urinary symptoms. Mobile genetic elements (MGEs), including plasmids and phages, within this niche have only recently begun to be explored. These MGEs can expand metabolic capacity and increase virulence, as well as confer antibiotic resistance. As such, they have the potential to contribute to urinary symptoms. While plasmids for some of the bacterial taxa found within the urinary microbiota (urobiome) have been well characterized, many urinary species are under-studied with few genomes sequenced to date. Using a two-pronged bioinformatic approach, we have conducted a comprehensive investigation of the plasmid content of urinary isolates representative of 102 species. The bioinformatic tools plasmidSPAdes and Recycler were used in tandem to identify plasmid sequences from raw short-read sequence data followed by manual curation. In total, we identified 603 high-confidence plasmid sequences in 20 different genera of the urobiome. In total, 70 % of these high-confidence plasmids exhibit sequence similarity to plasmid sequences from the gut. This observation is primarily driven by plasmids from E. coli , which is found in both anatomical niches. To confirm our bioinformatic predictions, long-read sequencing was performed for 23 of the E. coli isolates in addition to two E. coli strains that were sequenced as part of a prior study. Overall, 66.95 % of these predictions were confirmed highlighting the strengths and weaknesses of current bioinformatic tools. Future studies of the urobiome, especially concerning under-studied species in the urobiome, should employ long-read sequencing to expand the catalogue of plasmids for this niche.

Characterizing Plasmids in Bacteria Species Relevant to Urinary Health

The urinary tract has a microbial community (the urinary microbiota or urobiota) that has been associated with human health. Whole genome sequencing of bacteria is a powerful tool, allowing investigation of the genomic content of the urobiota, also called the urinary microbiome (urobiome). Bacterial plasmids are a significant component of the urobiome yet are understudied. Because plasmids can be vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. In this project, we sought plasmids in 11 clinically relevant urinary species: Aerococcus urinae, Corynebacterium amycolatum, Enterococcus faecalis, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Lactobacillus gasseri, Lactobacillus jensenii, Staphylococcus epidermidis, Streptococcus anginosus, and Streptococcus mitis. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in other species sequenced thus far. Some identified plasmidic assemblies were predicted to have putative virulence and/or antibiotic resistance genes, although the majority of their annotated coding regions were of unknown predicted function. In this study, we report on plasmids from urinary species as a first step to understanding the role of plasmids in the bacterial urobiota. IMPORTANCE The microbial community of the urinary tract (urobiota) has been associated with human health. Whole genome sequencing of bacteria permits examination of urobiota genomes, including plasmids. Because plasmids are vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. Currently, urobiota plasmids are understudied. Here, we sought plasmids in 11 clinically relevant urinary species. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in the other 6 species. We identified putative virulence and/or antibiotic resistance genes in some of the plasmidic assemblies, but most of their annotated coding regions were of unknown function. This is a first step to understanding the role of plasmids in the bacterial urobiota.

Brain perfusion and permeability in patients with advanced, refractory glioblastoma treated with lomustine and the transforming growth factor-β receptor I kinase inhibitor LY2157299 monohydrate

Transforming growth factor-β (TGF-β) signaling is associated with tumor progression and vascularization in malignant glioma. In the present study, magnetic resonance imaging was used to evaluate changes in the size and vascularity of glioblastomas in 12 patients who were treated with lomustine and the novel inhibitor of TGF-β signaling, LY2157299 monohydrate. A response in tumor size was observed in 2 of the 12 patients; in 1 of these 2 patients, a reduction in vascular permeability and perfusion was also detected. The effect was observed following 4 cycles of treatment (~3 months). Changes in vascularity have not previously been attributed to treatment with lomustine; therefore, the effect may be associated with LY2157299 treatment. LY2157299 does not appear to have an anti-angiogenic effect when combined with lomustine, and hence may have a different mechanism of action profile compared with anti-angiogenic drugs.

Spontaneous loss of antibiotic-resistant plasmids transferred to Escherichia coli in experimental chronic bladder infection

BACKGROUND

We investigated whether Escherichia coli that has been transformed with antibiotic-resistant plasmids spontaneously loses the plasmids while infecting the rat bladder.

METHODS

A nontransmissible antibiotic-resistant plasmid was transferred to a clinically isolated strain of E. coli. A knotted thread holding the strain was implanted into the bladder of male Wistar rats. One or 4 weeks later, the total number of bacteria and that of plasmid-carrying bacteria were measured in the bladder.

RESULTS

When plasmid-carrying E. coli alone was inoculated, most of the plasmid-carrying E. coli were replaced with plasmid-free E. coli. When plasmid-carrying and plasmid-free E. coli were simultaneously inoculated, this replacement was accelerated.

CONCLUSION

These results suggest that E. coli carrying antibiotic-resistant plasmids spontaneously lose the plasmids as time passes, and thus become sensitive to antibiotics.

Comparison of virulence factors and antibiotic resistance profiles of Escherichia coli strains from humans and dogs with urinary tract infections

The purpose of this study was to compare virulence factors and antibiotic resistance profiles of Escherichia coli strains isolated from dogs and humans with urinary tract infections. Factors studied included resistance to antibiotics and the transferability of R-plasmids to a recipient E. coli; production of colicins, hemolysins, beta-lactamase, and urease; hemagglutination of erythrocytes; and fermentation of dulcitol. The canine E. coli isolates had a wider range of antibiotic resistance and a higher R-plasmid transmissibility rate. A higher percentage of the canine isolates produced colicins (40% vs. 24%), hemolysins (44% vs. 16%), beta-lactamase (52% vs. 4%), and fermented dulcitol (84% vs. 80%) as compared with the human isolates. The human isolates had a greater ability to hemagglutinate erythrocytes as compared with the canine isolates (24% vs. 8%). None of the isolates produced urease.

Salmonella typhimurium strains carrying haemolysin plasmids and cloned haemolysin genes from Escherichia coli

Like all other Salmonella typhimurium strains examined, the smooth variants SF1397 (LT2) and 1366 and also their semi-rough and rough derivatives are non-haemolytic. Nevertheless, two haemolysin (Hly) plasmids of E. coli belonging to the inc groups incFIII,IV (pSU316) and incI2 (pHly152) were able to be introduced into these strains by conjugation and stably maintained. A considerable percentage of the Hly+ transconjugants obtained had lost parts of their O-side chains, a result of selection for the better recipient capability of "semi-rough" variants rather than the direct influence of the Hly+ plasmids themselves. In contrast to the incFIII,IV plasmid pSU316, which exhibited higher conjugation rates with rough recipients, the incI2 plasmid pHly152 was accepted best by smooth strains. Transformation with cloned E. coli haemolysin (hly) determinant was inefficient (less than 10(-6)) for smooth strains, but 10(2) - 10(3) times higher for rough recipients, and was increased by the use of Salmonella-modified DNA. The transformants and transconjugants were relatively stable and showed the same haemolytic activity as the E. coli donor strains. The virulence of the Hly+ smooth, semi-rough and rough S. typhimurium strains was tested in two mouse models, and neither the mortality rate nor the ability to multiply within the mouse spleen was influenced by the hly determinants.

Current mechanisms of resistance to antimicrobial agents in microorganisms causing infection in the patient at risk for infection

The mechanisms of resistance encountered in bacteria causing infection in the patient at risk for infection are diverse. Most resistance currently seen is the result of plasmid transfer rather than mutational events. However, extensive use of antimicrobial agents in the hospital has caused the selection of organisms resistant to many agents by virtue of chromosomally mediated mechanisms. Staphylococcus aureus resistant to beta-lactams due to altered penicillin-binding proteins has become a problem in certain patients such as narcotic addicts and chronic care facility patients exposed to many beta-lactam antibiotics. S. epidermidis has also proved to be a problem in patients with indwelling foreign devices, and altered penicillin-binding proteins also make these organisms resistant to available penicillins and cephalosporins. Streptococcus fecalis has become increasingly resistant to aminoglycosides, erythromycin, and tetracyclines due to plasmid-mediated enzymes. Hemophilus influenzae resistant to both penicillins and chloramphenicol by virtue of beta-lactamases and chloramphenicol transacetylase has been encountered. Beta-lactamase-mediated resistance of Enterobacteriaceae, Escherichia coli, and Klebsiella pneumoniae to beta-lactam antibiotics has increased, and resistance of Serratia marcescens and Pseudomonas aeruginosa to aminoglycosides and penicillins is a widespread phenomenon. Mechanisms to reduce resistance will include not only careful attention to hygienic practices but also more appropriate use of antibiotics selecting the proper agent depending on the type of patient and environment in which the infection develops.

Comparative in vitro activities of norfloxacin (MK-0366) and six commonly used antimicrobial agents against 199 urinary isolates showing various degrees of antibiotic resistance

The in vitro activity of norfloxacin (MK-0366), a new oral antimicrobial agent, was compared to that of ampicillin, tetracycline, cefazolin, nitrofurantoin, nalidixic acid, and trimethoprim against 199 gram-negative urinary isolates. Among these isolates were ampicillin-resistant Escherichia coli and gentamicin-resistant Pseudomonas aeruginosa and Serratia marcescens. Norfloxacin was the most active antimicrobial agent tested against all isolates studied; it was the only agent active against P. aeruginosa and S. marcescens.

Serum resistance among Escherichia coli strains causing urinary tract infection in relation to O type and the carriage of hemolysin, colicin, and antibiotic resistance determinants

The sensitivity to normal human serum of 91 smooth strains of Escherichia coli isolated from urinary tract infections was determined. Production of hemolysin, which was common and associated primarily with the types O4, O6, O18, and O75, was significantly correlated with high levels of serum resistance, both within the total population and within individual O types. In contrast, serum resistance was not significantly associated with antibiotic resistance (whether transmissible or not), with colicinogeny in general, or with colicin V production in particular. This indicates that the carriage of R and ColV plasmids, shown previously to be capable of conferring increased levels of serum resistance on individual strains of E. coli isolated from other sources, does not play an important part in determining the serum sensitivity of the E. coli population involved in urinary tract infection.