Infective endocarditis caused by Enterobacteriaceae: phenotypic and molecular characterization of Escherichia coli and Klebsiella pneumoniae in Rio de Janeiro, Brazil

The etiological agent for infective endocarditis (IE), a life-threatening disease, is usually gram-positive bacteria. However, gram-negative bacteria can rarely cause IE and 4% of cases are associated with morbidity and mortality. This study aimed to characterize Escherichia coli and Klebsiella pneumoniae isolates from the blood of patients with IE. The characteristics of blood isolates were compared with those of urinary isolates from patients with urinary tract infections (UTIs). The results of this study revealed that K. pneumoniae isolates from patients with IE were phylogenetically related to those from patients with UTI. Additionally, the resistance phenotype, resistance gene, virulence gene, and plasmid profiles were similar between the blood and urinary isolates. The isolates belonging to the sequence types (STs) 76, 36, 101 (K. pneumoniae), and 69 (E. coli) are reported to be associated with drug resistance. The Enterobacteriaceae isolates from patients with IE did not produce extended-spectrum β-lactamase or carbapenemase. Additionally, this study investigated the virulence phenotype, biofilm formation ability, and the ability to adhere to the epithelial cells in vitro of the isolates. The isolates from patients with IE exhibited weaker biofilm formation ability than the urinary isolates. All isolates from patients with IE could adhere to the renal epithelial cells. However, three isolates from patients with UTIs could not adhere to the epithelial cells. The closely related K. pneumoniae isolates (648, KP1, KP2, KP3, and KP4) could not form biofilms or adhere to the epithelial cells. In summary, the molecular analysis revealed that the genetic characteristics of IE-causing K. pneumoniae and E. coli were similar to those of UTI-causing isolates. These isolates belonged to the STs that are considered treatable. Genetically similar isolates did not exhibit the same virulence phenotype. Thus, these non-hypervirulent clones must be monitored as they can cause complex infections in susceptible hosts.

Corrigendum: Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil

[This corrects the article DOI: 10.3389/fmicb.2018.00243.].

Characterization of fosfomycin heteroresistance among multidrug-resistant Escherichia coli isolates from hospitalized patients in Rio de Janeiro, Brazil

OBJECTIVES

Urinary tract infections (UTIs) caused by multidrug-resistant Escherichia coli have become a major medical concern. Old antibiotics such as fosfomycin have become an alternative therapeutic option due to their effectiveness and, as a result, fosfomycin is now used as a first-line drug for the treatment of UTIs in many countries. Despite low resistance rates, fosfomycin heteroresistance, defined as a phenomenon where subpopulations of bacteria are resistant to high antibiotic concentrations whereas most of the bacteria are susceptible, is an underestimated problem.

METHODS

The frequency of heteroresistance in E. coli isolated from hospitalized patients in Brazil and its effect on susceptibility of E. coli in biofilms was studied and the isolates were molecularly characterized to reveal the mechanisms behind their fosfomycin heteroresistance using whole-genome sequencing.

RESULTS

A higher frequency of fosfomycin heteroresistance compared with other studies was found. In biofilms, most heteroresistant isolates were less sensitive to fosfomycin than control isolates and showed overexpression of metabolic genes thereby increasing their survival rate. Molecular characterization showed that some resistant subpopulations derived from heteroresistant isolates had a defect in their fosfomycin uptake system caused by mutations in transporter and regulatory genes, whereas others overexpressed the murA gene. None to minor effects on bacterial fitness were observed. Oxidative stress protection, virulence and metabolic genes were differentially expressed in resistant subpopulations and heteroresistant isolates.

CONCLUSION

Frequent detection of heteroresistance in UTIs may play a role in the failure of antibiotic treatments and should therefore be more carefully diagnosed.

Determining the Virulence Properties of Escherichia coli ST131 Containing Bacteriocin-Encoding Plasmids Using Short- and Long-Read Sequencing and Comparing Them with Those of Other E. coli Lineages

Escherichia coli ST131 is a clinical challenge due to its multidrug resistant profile and successful global spread. They are often associated with complicated infections, particularly urinary tract infections (UTIs). Bacteriocins play an important role to outcompete other microorganisms present in the human gut. Here, we characterized bacteriocin-encoding plasmids found in ST131 isolates of patients suffering from a UTI using both short- and long-read sequencing. Colicins Ia, Ib and E1, and microcin V, were identified among plasmids that also contained resistance and virulence genes. To investigate if the potential transmission range of the colicin E1 plasmid is influenced by the presence of a resistance gene, we constructed a strain containing a plasmid which had both the colicin E1 and blaCMY-2 genes. No difference in transmission range was found between transformant and wild-type strains. However, a statistically significantly difference was found in adhesion and invasion ability. Bacteriocin-producing isolates from both ST131 and non-ST131 lineages were able to inhibit the growth of other E. coli isolates, including other ST131. In summary, plasmids harboring bacteriocins give additional advantages for highly virulent and resistant ST131 isolates, improving the ability of these isolates to compete with other microbiota for a niche and thereby increasing the risk of infection.

Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil

Urinary tract infections (UTIs) are often caused by Escherichia coli. Their increasing resistance to broad-spectrum antibiotics challenges the treatment of UTIs. Whereas, E. coli ST131 is often multidrug resistant (MDR), ST69 remains susceptible to antibiotics such as cephalosporins. Both STs are commonly linked to community and nosocomial infections. E. coli phylogenetic groups B2 and D are associated with virulence and resistance profiles making them more pathogenic. Little is known about the population structure of E. coli isolates obtained from urine samples of hospitalized patients in Brazil. Therefore, we characterized E. coli isolated from urine samples of patients hospitalized at the university and three private hospitals in Rio de Janeiro, using whole genome sequencing. A high prevalence of E. coli ST131 and ST69 was found, but other lineages, namely ST73, ST648, ST405, and ST10 were also detected. Interestingly, isolates could be divided into two groups based on their antibiotic susceptibility. Isolates belonging to ST131, ST648, and ST405 showed a high resistance rate to all antibiotic classes tested, whereas isolates belonging to ST10, ST73, ST69 were in general susceptible to the antibiotics tested. Additionally, most ST69 isolates, normally resistant to aminoglycosides, were susceptible to this antibiotic in our population. The majority of ST131 isolates were ESBL-producing and belonged to serotype O25:H4 and the H30-R subclone. Previous studies showed that this subclone is often associated with more complicated UTIs, most likely due to their high resistance rate to different antibiotic classes. Sequenced isolates could be classified into five phylogenetic groups of which B2, D, and F showed higher resistance rates than groups A and B1. No significant difference for the predicted virulence genes scores was found for isolates belonging to ST131, ST648, ST405, and ST69. In contrast, the phylogenetic groups B2, D and F showed a higher predictive virulence score compared to phylogenetic groups A and B1. In conclusion, despite the diversity of E. coli isolates causing UTIs, clonal groups O25:H4-B2-ST131 H30-R, O1:H6-B2-ST648, and O102:H6-D-ST405 were the most prevalent. The emergence of highly virulent and MDR E. coli in Brazil is of high concern and requires more attention from the health authorities.