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Investigating antibiotics, antibiotic resistance genes, and microbial contaminants in groundwater in relation to the proximity of urban areas.

Groundwater is an essential public and drinking water supply and its protection is a goal for global policies. Here, we investigated the presence and prevalence of antibiotic residues, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and microbial contamination in groundwater environments at various distances from urban areas. Antibiotic concentrations ranged from below detection limit to 917 ng/L, being trimethoprim, macrolide, and sulfonamide the most abundant antibiotic classes. A total of eleven ARGs (aminoglycoside, β-lactam, chloramphenicol, Macrolide-Lincosamide-Streptogramin B - MLSB, sulfonamide, and tetracycline), one antiseptic resistance gene, and two MGEs were detected by qPCR with relative abundances ranging from 6.61 × 10to 2.30 × 10copies/16S rRNA gene copies. ARGs and MGEs were widespread in the investigated groundwater environments, with increased abundances not only in urban, but also in remote areas. Distinct bacterial community profiles were observed, with a higher prevalence of Betaproteobacteria and Bacteroidetes in the less-impacted areas, and that of Firmicutes in the contaminated groundwater. The combined characteristics of increased species diversity, distinct phylogenetic composition, and the possible presence of fecal and/or pathogenic bacteria could indicate different types of contamination. Significant correlations between ARGs, MGEs and specific taxa within the groundwater bacterial community were identified, revealing the potential hosts of resistance types. Although no universal marker gene could be determined, a co-selection of int1, qacEΔ1 and sulI genes, a proxy group for anthropogenic pollution, with the tetC, tetO, tetW resistance genes was identified. As the tet group was observed to follow the pattern of environmental contamination for the groundwater samples investigated in this study, our results strongly support the proposal of this group of genes as an environmental tracer of human impact. Overall, the present study investigated several emerging contaminants in groundwater habitats that may be included in monitoring programs to enable further regulatory and protection measures.

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Evaluation of the frequency of Candida spp. in hospitalized and non-hospitalized subjects.

The aim of this study was to evaluate the frequency of Candida species between a non-hospitalized and a hospitalized population. For this purpose, samples of saliva were sampled through sterile swabs, moistened in peptone water and rubbed in the oral cavity of 140 individuals, from which, 70 were hospitalized patients from the Medical Clinic of a Teaching Hospital and the other 70 were non-hospitalized subjects. All saliva samples were plated in Sabouraud Dextrose agar added with Chloramphenicol and incubated at 36 °C for 48 hours. The morphology identification was performed through macroscopic and microscopic characterization, the CHROMagar Candida medium and the VITEK® system Yeast Biochemical Card (bio Mérieux SA, France). The results showed a colonization of Candida spp. in 85.7% the hospitalized individuals, where the species found were C. albicans (60%), C. tropicalis (23.4%), C. krusei (3.3%) and Candida spp. (13.3%). In the non-hospitalized individuals the colonization by Candida spp was 47.1%, and the species found were: C. albicans (45.5%), C.krusei (9.1%), C. guilliermondii (9.1% %), C. tropicalis (3.0%), C. famata (3.0%) and Candida spp. (30.3%). In spite of their presence in oral cavity in both groups, Candida spp. was more frequently isolated in hospitalized individuals, who were 6.73 times more likely to have this fungus in the oral cavity and were 3.88 times more likely to have Candida albicans.

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Whole genome sequencing of multidrug-resistantserovar Typhimurium isolated from humans and poultry in Burkina Faso.

Multidrug-resistantis an important cause of morbidity and mortality in developing countries. The aim of this study was to characterize and compare multidrug-resistantserovar Typhimurium isolates from patients and poultry feces.

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The prevalence and antimicrobial resistance of Listeria spp in raw milk and traditional dairy products delivered in Yazd, central Iran (2016).

Listeria monocytogenes is an important foodborne pathogen which its data in Iranian dairy products is limited. A total of 545 samples of traditional dairy products (raw milk, traditional cheese, traditional butter, traditional curd, and traditional ice cream) were collected from traditional dairy shops located in Yazd, Iran. L. monocytogenes was isolated, and positive samples were confirmed by polymerase chain reaction. Antibiotic sensitivity test was conducted to determine the antibiotic resistance. Listeria species were isolated from 11.7% samples. 4.03% samples were identified as L. monocytogenes, 5.6% as L. innocua, 1.8% as L. seeligeri, and 0.18% L. murrayi. All L. monocytogenes isolates were resistant to tetracycline, chloramphenicol, penicillin, and amoxicillin/clavulanic acid. Consumption of raw milk and its traditional products prepared inadequate heat treatment and the lack of appropriate control measures might lead to serious health problems. As our results show, the Iranian food safety authorities should set up an effective standard to screen all susceptible food for the presence of Listeria spp.

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Molecular characterization of multidrug pneumococcal clones colonizing healthy children in Mérida, Venezuela.

We analyzed genetics mechanisms of antibiotics resistance, clonal composition and pili in forty eight MDR-pneumococci isolated from healthy children in Mérida, Venezuela. Intermediate resistance to penicillin was related to variations on pbp2b and pbp2x genes. High-level resistance to penicillin, low susceptibility to cephalosporins and carbapenems were associated with alterations on pbp1a, pbp2b and pbp2x genes. Non-beta-lactam resistance was associated with Tn3872, Tn5253, Tn6002, Tn2010 transposons. Macrolide-resistant strains carried ermB or mefE, but not the mefA gene. Tetracycline and chloramphenicol-resistant pneumococci carried tetM and cat genes, respectively. MDR- pneumococci were related to 6 clonal complexes (CCs), largely CC156 or CC15. A limited diversity on pbp2a,2b,2x-RFLP profile within each clone was observed. Conversely, the detection of non-beta-lactam resistance and transposons revealed a clear genetic diversity within clones. We found a group of nontypeable/cpsA-negative pneumococci related to the Null Capsule Clade 1 (NCC1) carrying a Tn2009-element. Each NCC1-related strain showed a novel MLST allelic combination and a different pbp2a,2b,2x-RFLP profile. PI-1 (Pilus type 1 rrgC gene) was present in most of the MDR-pneumococci and its occurrence was commonly homogeneous within each clone. PI-1 was present in all CC242 and CC320 pneumococci whereas it was absent in all CC37, CC81 and NCC1 isolates. CC156 and CC15 isolates showed variations on the occurrence of PI-1. Both PI-1 and the islet for pilus type 2 were present in CC230 isolates. We provide useful data to follow the evolution of clonal composition, mechanism of antibiotics resistance and the occurrence of pili among pneumococci circulating in Mérida, Venezuela.

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Antibiotic resistance and molecular characterization of Shigella isolates recovered from children less than 5 years in Manhiça, Southern Mozambique.

The objective of the study was to assess antibiotic resistance and the molecular epidemiology of Shigella isolates from a case-control study of diarrhea, conducted from 2007-2012 in children less than 5 years of age in Manhiça district, southern Mozambique. All isolates were tested for antimicrobial susceptibility using the disc-diffusion method. PCR was used to detect different molecular mechanisms of antibiotic resistance. Serotyping was performed using specific antisera. The clonal relationship of S. flexneri and S. sonnei was assessed by Pulsed-Field Gel Electrophoresis (PFGE). Of the 67 Shigella isolates analyzed, 59 were diarrheal cases and 8 controls. S. flexneri (70.1%; 47/67) was the most frequent species followed by S. sonnei (23.9%; 16/67).The most prevalent S. flexneri serotypes were 2a (38.3%; 18/47), 6 (19.2%; 9/47) and 1b (14.9%; 7/47). High rates of antimicrobial resistance were observed for trimethoprim/ sulfametoxazole (92.5%; 62/67), tetracycline (68.7%; 46/67), chloramphenicol (53.7%; 36/67) and ampicillin (50.7%; 34/67). Multidrug resistance was present in 55.2% (37/67) of the isolates and was associated with an 8.1% (3/37) case fatality rate. PFGE revealed 22 clones (16 S. flexneri and 6 S. sonnei), among which, P1 (31.9%; 15/47), P9 (17%; 8/47) and P2 (10.6%; 5/47) were the most prevalent S. flexneri clones. In conclusion, S. flexneri was the most prevalent species with MDR isolates mainly belonging to three specific clones (P1, P9 and P2). The case fatality rate observed among MDR isolates is a matter of concern indicating the need for appropriate treatment.

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In Vitro Evaluation of Probiotic Potential of Lactic Acid Bacteria Isolated from Yunnan De'ang Pickled Tea.

This study aimed to investigate the probiotic potential of lactic acid bacteria (LAB) strains isolated from De'ang pickled tea, a traditional food consumed by the De'ang nationality of Yunnan, China. Twenty-six LAB strains isolated from De'ang pickled tea were subjected to identification based on 16S rRNA gene sequence analysis. Twenty-four belonged to Lactobacillus plantarum, one belonged to Enterococcus casseliflavus, and one belonged to Lactobacillus acidophilus. Eighteen out of 26 LAB strains which showed a higher capability to tolerate simulated gastrointestinal juices were chosen to further evaluate their probiotic properties. Varied adhesive abilities and auto-aggregative capacities of selected LAB strains were dependent on species and even strains. All tested LAB strains were resistant to kanamycin, streptomycin, gentamycin, and vancomycin and sensitive to tetracycline and chloramphenicol. Ten out of the 18 strains are resistant to ampicillin, and the remaining strains are sensitive to ampicillin; 4 out of the 18 strains showed resistance to erythromycin. Compared to reference strain Lactobacillus rhamnosus strain GG, these LAB strains had a greater or comparative antimicrobial activity against Salmonella typhimurium or Escherichia coli. In contrast, eight out of the 18 strains suppressed growth of Shigella flexneri. Two L. plantarum strains, ST and STDA10, not only exhibited good probiotic properties but also showed a good ability of scavenging DPPH and ABTS. This study suggests that L. plantarum ST and STDA10 could be used as potential probiotics applied in functional foods.

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Virulence Determinants and Antimicrobial Resistance Patterns of Vancomycin-resistantIsolated from Different Sources in Southwest Iran.

This study aimed to investigate the incidence of antibiotic-resistance and virulence genes in vancomycin-resistantisolated from different sources in southwest Iran from Mar to Sep 2015.

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Chlorinated Azaphilone Pigments with Antimicrobial and Cytotoxic Activities Isolated from the Deep Sea Derived Fungus Chaetomium sp. NA-S01-R1.

Four novel compounds, chaephilone C (), chaetoviridides A-C (-), were obtained from the culture of a deep sea derived fungussp. NA-S01-R1, together with four known compounds-chaetoviridin A (), chaetoviridine E (), chaetomugilin D () and cochliodone A (). Their structures, including absolute configurations, were assigned based on NMR, MS and time-dependent density functional theory (TD-DFT) ECD calculations. A plausible biogenetic pathway for compounds-was proposed. Compoundsandexhibited antibacterial activities againstand. Compounds,anddisplayed similar anti-methicillin resistant(anti-MRSA) activities in comparison to chloramphenicol. Compoundshowed the most potent cytotoxic activities towards the Hep G2 cell and compoundsanddemonstrated relatively stronger cytotoxic activities than the other compounds against the HeLa cell.

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Diversity and Antimicrobial Resistance Genotypes in Non-Typhoidal Salmonella Isolates from Poultry Farms in Uganda.

Non-typhoidal(NTS) are foodborne pathogens of global public health significance. The aim of this study was to subtype a collection of 85 NTS originating from poultry farms in Uganda, and to evaluate a subgroup of phenotypically resistant isolates for common antimicrobial resistance genes and associated integrons. All isolates were subtyped by pulsed-field gel electrophoresis (PFGE). Phenotypically resistant isolates (= 54) were screened by PCR for the most relevant AMR genes corresponding to their phenotypic resistance pattern, and all 54 isolates were screened by PCR for the presence of integron class 1 and 2 encoding genes. These genes are known to commonly encode resistance to ampicillin, tetracycline, ciprofloxacin, trimethoprim, sulfonamide and chloramphenicol. PFGE revealed 15 pulsotypes representing 11 serotypes from 75 isolates, as 10 were non-typable. Thirty one (57.4%) of the 54 resistant isolates carried at least one of the seven genes (identified by PCR and six (11%) carried class 1 integrons. This study has shown that a diversity of NTS-clones are present in Ugandan poultry farm settings, while at the same time similar NTS-clones occur in different farms and areas. The presence of resistance genes to important antimicrobials used in human and veterinary medicine has been demonstrated, hence the need to strengthen strategies to combat antimicrobial resistance at all levels.

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