Genomic analysis of a novel phage vB_SenS_ST1UNAM with lytic activity against Salmonella enterica serotypes.

In this study, we present the complete annotated genome of a novel Salmonella phage, vB_SenS_ST1UNAM. This phage exhibits lytic activity against several Salmonella enterica serotypes, such as S. Typhi, S. Enteritidis, and S. Typhimurium strains, which are major causes of foodborne illness worldwide. Its genome consists of a linear, double-stranded DNA of 47,877 bp with an average G+C content of 46.6%. A total of 85 coding regions (CDS) were predicted, of which only 43 CDS were functionally assigned. Neither genes involved in the regulation of lysogeny, nor antibiotic resistance genes were identified. This phage harbors a lytic cassette that encodes a type II-holin and a Rz/Rz1-like spanin complex, along with a restriction-modification evasion system and a depolymerase that degrades Salmonella exopolysaccharide. Moreover, the comparative analysis with closely related phage genomes revealed that vB_SenS_ST1UNAM represents a novel genus, for which the genus "Gomezvirus" within the subfamily "ST1UNAM-like" is proposed.

Genomic characterization of two bacteriophages (vB_EcoS-phiEc3 and vB_EcoS-phiEc4) belonging to the genus Kagunavirus with lytic activity against uropathogenic Escherichia coli.

In this study, the genomes of two lytic bacteriophages, vB_EcoS-phiEc3 and vB_EcoS-phiEc4, were sequenced and characterized using bioinformatics approaches. Whole-genome analysis showed that both phages belonged to the Kagunavirus genus, Guernseyvirinae subfamily and Siphoviridae family. Moreover, their genomes had 45, 288 bp and 44,540 bp, and G + C content of 48.42% and 50.04%, respectively. The genome of vB_EcoS-phiEc3 harbored 80 protein coding sequences (CDSs), whereas vB_EcoS-phiEc4 harbored 75 CDSs. Among them, 50 CDSs in vB_EcoS-phiEc3 and 44 CDSs in vB_EcoS-phiEc4 were considered as functional genes. Their lytic activity against multidrug-resistant uropathogenic Escherichia coli (UPEC) strains, as well as the absence of antibiotic resistance genes, lysogenic and virulence genes, enable vB_EcoS-phiEc3 and vB_EcoS-phiEc4 as a safe therapy option against UPEC infections.

Patrones de adherencia en células HEp-2 de cepas de Escherichia coli aisladas de ríos contaminados de La Habana / Adherence patterns in HEp-2 cells of Escherichia coli strains isolated from contaminated rivers in Havana

Introducción: El proceso de adherencia es fundamental en el desarrollo de la mayoría de las infecciones ocasionadas por Escherichia coli. Para los patotipos de esta especie se describen tres patrones de adherencia diferentes: adherencia localizada, adherencia difusa y adherencia agregativa, los cuales se relacionan con los procesos patogénicos específicos que ocasiona en la clínica. Sin embargo, son pocos los estudios en relación con los fenotipos de adherencia in vitro de E. coli aisladas del ambiente. Objetivo: Determinar los fenotipos de adherencia de cepas de E. coli aisladas de ecosistemas dulceacuícolas de La Habana. Métodos: Se analizaron 108 cepas de E. coli aisladas de los ríos Almendares, Quibú y Luyanó de La Habana. Se determinó el patrón de adherencia mediante ensayos de adherencia en cultivo celular de la línea HEp-2 así como el serotipo de cada cepa. Resultados: El 25 por ciento de las cepas de E. coli aisladas fueron adherentes y el 75 por ciento fueron no adherentes. Veintidós cepas mostraron el típico patrón de adherencia difusa y cinco cepas mostraron una adherencia agregativa. Se encontraron cepas de los dos patrones de adherencia en los tres ríos evaluados. Las cepas presentaron 24 serotipos diferentes. Conclusiones: Se demostró que las cepas de E. coli ambientales circulantes en estos ecosistemas presentan características adherentes, cuya patogenicidad implica un riesgo potencial para la salud humana, especialmente en edades pediátricas(AU)

Introduction: Adherence is crucial to the development of most Escherichia coli infections. Three different adherence patterns have been described for pathotypes of this species: localized, diffuse and aggregative adherence, based on the specific clinical pathogenic processes they bring about. However, few studies have been conducted about in vitro adherence phenotypes of E. coli isolated from the environment. Objective: Determine the adherence phenotypes of E. coli strains isolated from freshwater ecosystems in Havana. Methods: An analysis was conducted of 108 E. coli strains isolated from the rivers Almendares, Quibú and Luyanó in Havana. Determination was made of the adherence pattern by adherence assays in HEp-2 cell line cultures, as well as of the serotype for each strain. Results: Of the E. coli strains isolated, 25 percent were adherent and 75 percent were not. Twenty-two strains displayed the typical diffusely adherent pattern and five displayed aggregative adherence. Strains exhibiting the two adherence patterns were found in the three rivers evaluated. The strains contained 24 different serotypes. Conclusions: The environmental E. coli strains circulating in these ecosystems were found to have adherent characteristics whose pathogenicity implies a potential risk to human health, particularly in childhood(AU)

|Isolation and characterization of novel bacteriophages as a potential therapeutic option for Escherichia coli urinary tract infections.

Urinary tract infections (UTIs) are mainly caused by uropathogenic Escherichia coli (UPEC), whose impact can be exacerbated by multidrug-resistant (MDR) strains. Effective control strategies are, therefore, urgently needed. Among them, phage therapy represents a suitable alternative. Here, we describe the isolation and characterization of novel phages from wastewater samples, as well as their lytic activity against biofilm and adherence of UPEC to HEp-2 cells. The results demonstrated that phage vB_EcoM-phiEc1 (ϕEc1) belongs to Myoviridae family, whereas vB_EcoS-phiEc3 (ϕEc3) and vB_EcoS-phiEc4 (ϕEc4) belong to Siphoviridae family. Phages showed lytic activity against UPEC and gut commensal strains. Phage ϕEc1 lysed UPEC serogroups, whereas phages ϕEc3 and ϕEc4 lysed only UTI strains with higher prevalence toward the O25 serogroup. Moreover, phages ϕEc1 and ϕEc3 decreased both biofilm formation and adherence, whereas ϕEc4 was able to decrease adherence but not biofilm formation. In conclusion, these novel phages showed the ability to decrease biofilm and bacterial adherence, making them promising candidates for effective adjuvant treatment against UTIs caused by MDR UPEC strains. KEY POINTS: Phage with lytic activity against MDR UPEC strains were isolated and characterized under in vitro conditions. A novel method was proposed to evaluate phage activity against bacterial adherence in HEp-2 cell.. Phages represent a suitable strategy to control infections caused by MDR bacteria.

Association of phylogenetic distribution and presence of integrons with multidrug resistance in Escherichia coli clinical isolates from children with diarrhoea.

BACKGROUND: Escherichia coli strains include both commensal and virulent clones distributed in different phylogenetic groups. Antimicrobial resistance is an increasingly serious public health threat at the global level and integrons are important mobile genetic elements involved in resistance dissemination. This paper aims to determine the phylogenetic groups and presence of class 1 (intl1) and 2 (intl2) integrons in E. coli clinical isolates from children with diarrhoea, and to associate these characteristics with their antimicrobial resistance. METHODS: Phylogeny and presence of integrons (intl1 and intl2) were analysed by PCR and amplicon sequencing in 70 E. coli isolates from children with and without diarrhoea (35 of each group) from Sinaloa, Mexico; these variables were analysed for correlation with the antimicrobial resistance profile of the isolates. RESULTS: The most frequent phylogroups were A (42.9%) and B2 (15.7%). The E. coli isolates from children with diarrhoea were distributed in all phylogroups; while strains from children without diarrhoea were absent from phylogroups C, E, and clade I. The 17.1% of the isolates carried integrons (15.7% intI1 and 1.4% intI2); 28.6% of the isolates from children with diarrhoea showed the class 1 integron. Strains of phylogroup A showed the highest frequency of integrons (33.3%). The association of multidrug resistance and the presence of integrons was identified in 58.3% of strains isolated from children with diarrhoea included in phylogroups A and B2. The sequence analysis of intl1 and intl2 showed silent point mutations and similarities with plasmids of some APEC and AIEC strains. CONCLUSION: Commensal E. coli strains are potential disseminators of antimicrobial resistance, and the improvement in the use of antimicrobials to treat childhood diarrhoea is essential for the control of such resistance.

High prevalence of multidrug-resistant Escherichia coli isolates from children with and without diarrhoea and their susceptibility to the antibacterial activity of extracts/fractions of fruits native to Mexico.

PURPOSE: This paper aims to evaluate the antimicrobial resistance of Esherichia coli isolates from children under 5 years old, with and without diarrhoea, who were hospital outpatients in Culiacan, Sinaloa, Mexico. It also looks at the antimicrobial activity of fruit extracts against selected multidrug-resistant (MDR) E. coli strains. METHODOLOGY: A total of 205 E. coli isolates from stool samples were collected from 94 children under 5 years old who were outpatients from two hospitals in the city of Culiacan, Sinaloa, Mexico, during the autumn/winter of 2003/04; their resistance profiles to 19 commercial antimicrobials were investigated using the Kirby-Bauer method. The antibacterial activities of extracts/fractions of fruits (i.e. uvalama, Vitex mollis; ayale, Crescentia alata; and arrayan, Psidium sartorianum) were evaluated using the broth microdilution method. RESULTS: All E. coli isolates were susceptible to amikacin, nitrofurantoin and meropenem, and approximately 96 % were resistant to at least one antimicrobial, especially carbenicillin (93.2 %), cefuroxime sodium (53.7 %), ampicillin (40 %) and trimethoprim/sulfamethoxazole (35.1 %). Likewise, the frequency of MDR strains (44.9 %) was high, and no significant association with diarrhoea symptoms was found. Remarkably, all fruit extracts/fractions showed antibacterial activity against some, but not all, MDR isolates. The lowest minimal inhibitory concentration values were for the hexane fraction of arrayan (0.25 mg ml-1). CONCLUSION: A high number of antimicrobial-resistant E. coli (especially to ß-lactams and sulfonamides) and MDR isolates were detected in children under 5 years old, irrespective of diarrhoea symptoms; this is novel information for Culiacan, Sinaloa, Mexico. Moreover, our results showed that the studied fruit extracts/fractions are potential alternative or complementary treatments for MDR E. coli strains.

Microbiological Quality of Fresh Nopal Juice.

The consumption of fresh nopal cactus juice is widely popular among health-conscious consumers in Mexico. The juice is prepared from fresh cladodes that have only been rinsed with tap water and are not subjected to a pasteurization or terminal bacterial reduction process. The aim of this study was to evaluate the microbial quality of commercially available fresh juices (n = 162) made with nopal in Texcoco, State of Mexico, during the summer and spring season. Standard microbiological methods, the PCR technique and the serological method were used for isolation and identification of bacteria. All samples contained total coliforms and 91% were positive for Escherichia coli. Although total coliforms and E. coli were detected throughout the study, their populations were significantly lower (p < 0.05) in winter and spring, respectively. Citrobacter youngae was found in 20% of the samples, an unidentified species of Citrobacter in 10%, C. freundii and Proteus mirabilis in 3%, and Salmonella Javiana in 1%. The presence of these microorganisms, especially Salmonella, in the nopal juices is unacceptable due to its health significance. The information generated in this study is relevant for human health risk assessment associated with the consumption of unpasteurized nopal juices and potential interventions to minimize pathogen contamination.