Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities.

The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities.

Longitudinal Surveillance of Antibiotic Resistance in Escherichia coli and Enterococcus spp. from a Wastewater Treatment Plant and Its Associated Waters in KwaZulu-Natal, South Africa.

We assessed the prevalence, distribution, and antibiotic resistance patterns of Escherichia coli and Enterococcus spp. isolated from raw and treated wastewater of a major wastewater treatment plant (WWTP) in KwaZulu-Natal, South Africa and the receiving river water upstream and downstream from the WWTP discharge point. Escherichia coli and enterococci were isolated and counted using the Colilert®-18 Quanti-Tray® 2000 and Enterolert®-18 Quanti-Tray 2000 systems, respectively. A total of 580 quantitative PCR-confirmed E. coli and 579 enterococci were randomly chosen from positive samples and tested for in vitro antibiotic susceptibility using the disk diffusion assay against 20 and 16 antibiotics, respectively. The removal success of the bacterial species through the treatment procedure at the WWTP was expressed as log removal values (LRVs). Most E. coli were susceptible to meropenem (94.8%) and piperacillin-tazobactam (92.9%), with most Enterococcus susceptible to ampicillin (97.8%) and vancomycin (96.7%). In total, 376 (64.8%) E. coli and 468 (80.8%) Enterococcus isolates showed multidrug resistance (MDR). A total of 42.4% (246/580) E. coli and 65.1% (377/579) enterococci isolates had multiple antibiotic resistance indices >0.2. The LRV for E. coli ranged from 2.97 to 3.99, and for enterococci the range was observed from 1.83 to 3.98. A high proportion of MDR E. coli and enterococci were present at all sampled sites, indicating insufficient removal during wastewater treatment. There is a need to appraise the public health risks associated with bacterial contamination of environmental waters arising from such WWTPs to protect the health of users of the receiving water bodies.

Characterization of potentially probiotic lactic acid bacteria and bifidobacteria isolated from human colostrum.

Breast milk is the main source of nutrition for infants; it contains considerable microflora that can be transmitted to the infant endogenously or by breastfeeding, and it plays an important role in the maturation and development of the immune system. In this study, we isolated and identified lactic acid bacteria (LAB) from human colostrum, and screened 2 strains with probiotic potential. The LAB isolated from 40 human colostrum samples belonged to 5 genera: Lactobacillus, Bifidobacterium, Streptococcus, Enterococcus, and Staphylococcus. We also isolated Propionibacterium and Actinomyces. We identified a total of 197 strains of LAB derived from human colostrum based on their morphology and 16S rRNA sequence, among them 8 strains of Bifidobacterium and 10 strains of Lactobacillus, including 3 Bifidobacterium species and 4 Lactobacillus species. The physiological and biochemical characteristics of strains with good probiotic characteristics were evaluated. The tolerances of some of the Bifidobacterium and Lactobacillus strains to gastrointestinal fluid and bile salts were evaluated in vitro, using the probiotic strains Bifidobacterium lactis BB12 and Lactobacillus rhamnosus GG as controls. Among them, B. lactis Probio-M8 and L. rhamnosus Probio-M9 showed survival rates of 97.25 and 78.33% after digestion for 11 h in artificial gastrointestinal juice, and they exhibited growth delays of 0.95 and 1.87 h, respectively, in 0.3% bile salts. These two strains have the potential for application as probiotics and will facilitate functional studies of probiotics in breast milk and the development of human milk-derived probiotics.

Genome Analysis of Enterococcus mundtii Pe103, a Human Gut-Originated Pectinolytic Bacterium.

Pectin exists in significant amounts in vegetables and fruits as a component of the plant cell wall. In human diet, pectin is not degraded by the human digestive enzymes due to its complex structure; only gut bacteria degrade pectin in the large intestine. To date, although pectin is one of the most important sources of dietary fiber in human diet, there have been only few reports on human gut-originated pectinolytic bacteria. In this study, the strain Enterococcus mundtii Pe103, a bacterium with pectin-degrading activity, was isolated from the feces of a healthy Korean adult female. Culture experiments revealed that it could grow on pectin as the sole carbon source by degrading pectin to approximately 35% within 13 h. We report the complete genome data of human gut E. mundtii Pe103. It consists of a circular chromosome (3,084,146 bps) and two plasmids (63,713 and 56,223 bps). Genomic analysis suggested that at least nine putative enzymes related to pectin degradation are present in E. mundtii Pe103. These enzymes may be involved in the degradation of pectin. The whole genome information of E. mundtii Pe103 could improve the understanding of the mechanism underlying the degradation of pectin by human gut microbiota.

Use of microbiological and patient data for choice of empirical antibiotic therapy in acute cholangitis.

BACKGROUND: Ineffective antibiotic therapy increases mortality of acute cholangitis. The choice of antibiotics should reflect local resistance patterns and avoid the overuse of broad-spectrum agents. In this study, we analysed how results of bile and blood cultures and patient data can be used for selection of empirical antibiotic therapy in acute cholangits. METHODS: Pathogen frequencies and susceptibility rates were determined in 423 positive bile duct cultures and 197 corresponding blood cultures obtained from 348 consecutive patients with acute cholangitis. Patient data were retrieved from the medical records. Associations of patient and microbiological data were assessed using the Chi-2 test and multivariate binary logistic regression. RESULTS: In bile cultures, enterobacterales and enterococci were isolated with equal frequencies of approximately 30% whereas in blood cultures, enterobacterales predominated (56% compared to 21% enterococci). Antibiotic resistance rates of enterobacterales were > 20% for fluorochinolones, cephalosporines and acylureidopenicillins but not for carbapenems (< 2%). The efficacy of empirical therapy was poor with a coverage of bacterial bile and blood culture isolates in 51 and 69%, respectively. By multivariate analysis, predictors for pathogen species, antibiotic susceptibility and expected antibiotic coverage were identified. CONCLUSIONS: In unselected patients treated for acute cholangitis in a large tertiary refferential center, use of carbapenems seems necessary to achieve a high antibiotic coverage. However, by analysis of patient and microbiological data, subgroups for highly effective carbapenem-sparing therapy can be defined. For patients with community-acquired cholangitis without biliary prosthesis who do not need intensive care, piperacillin/tazobactam represents a regimen with an expected excellent antibiotic coverage.

ENTEROCOCCUS ENDOPHTHALMITIS: Clinical Settings, Antimicrobial Susceptibility, and Management Outcomes.

PURPOSE: To report the clinical presentation and management outcome of patients with endophthalmitis caused by Enterococcus species and to report the susceptibility profile of the isolates. METHODS: Twenty-nine cases with culture-proven Enterococcus endophthalmitis from January 2005 to May 2018 underwent vitrectomy/vitreous biopsy, intravitreal antibiotic with or without additional procedures. The undiluted vitreous was subjected to microbiologic evaluation. A favorable anatomical outcome was defined as preservation of the globe, absence of hypotony, attached retina, and absence of active inflammation at the last visit. Favorable visual outcome was final visual acuity ≥20/400. RESULTS: There were 24 men (82.8%). Mean age at presentation was 32.89 ± 25.25 years (median 24 years). Inciting event was open globe injury in 18 (62%), endogenous in 5 (17.24%), postcataract surgery in 3 (10.34%), postscleral buckling in 2 (6.89%), and postkeratoplasty in 1 (3.44%). Enterococcus casseliflavus was the commonest species isolated (14/29, 48.27%) followed by E. faecalis (9/29, 31%). Susceptibility to vancomycin was seen in 27/29 isolates (93%). Visual acuity was ≤20/400 in all eyes at presentation and ≥20/400 in 10/29 cases (34.48%) at final visit. Anatomical success was seen in 18/29 eyes (62%). Corneal involvement was high at 24/29 eyes (82.75%). CONCLUSION: Enterococcus is not an uncommon organism in the setting of endophthalmitis after open globe injury. Resistance to vancomycin is rare. Multidrug resistance pattern is restricted to E. faecalis. Visual outcome is poor despite early and appropriate therapy due to inherent organism virulence.

Eutrophication and Related Antibiotic Resistance of Enterococci in the Minjiang River, China.

Antimicrobial resistance (AMR) in the aquatic environment has received increasing attention in recent years, and growing eutrophication problems may contribute to AMR in aquatic ecosystems. To evaluate whether and how eutrophication affects AMR, 40 surface water samples were collected from the Minjiang River, Fujian Province, China. Total nitrogen (TN), total phosphorus (TP), and chemical oxygen demand (CODMn) were measured as eutrophication factors. Additionally, enterococci species were isolated and their resistance to six common antibiotics was tested. Eutrophication generally showed a trend of increasing with the flow direction of the Minjiang River, with 25 sites (62.5%) having a TN/TP value over the Redfield value (16:1), which indicated that eutrophication in this region was of phosphorus limitation. High nutrition sites were in or near urban areas. Poor quality water was found in the middle and lower reaches of the Minjiang River system. The resistance frequency of 40 enterococci isolates to the six antibiotics tested was as follows: oxytetracycline > erythromycin > ciprofloxacin > chloramphenicol > ampicillin > vancomycin (70, 50, 17.5, 12.5, 2.5, 0%), and the multi-resistant rate reached 50% with eight resistance phenotypes. AMR also increased along the direction of water flow downstream, and most of the sites with the highest AMR were in or near urban areas, as was true for nutrition levels. Positive correlations between AMR and eutrophication factors (TN, TP, and CODMn) were identified using the Pearson's correlation coefficient, and TN/TP generally was negatively related to AMR. These results indicated that eutrophication may induce or selective for resistance of water-borne pathogens to antibiotics, with a high resistance level and a wide resistance spectrum.

Pharmacodynamics of daptomycin in combination with other antibiotics for the treatment of enterococcal bacteraemia.

Daptomycin is commonly prescribed in combination with other antibiotics for treatment of enterococcal bacteraemia. Whilst a free drug area under the concentration-time curve to minimum inhibitory concentration (fAUC/MIC) ratio >27.4 is associated with 30-day survival with daptomycin monotherapy, it is unknown whether receipt of other antibiotics affects this threshold. Data were pooled from seven published trials assessing outcomes in daptomycin-treated enterococcal bacteraemia, including patients receiving daptomycin (≥72 h) and any ß-lactam, intravenous aminoglycoside, linezolid, tigecycline and/or vancomycin. Exposures were calculated using a published population pharmacokinetic model based on creatinine clearance, 90% protein binding and daptomycin Etest MIC. The fAUC/MIC threshold predictive of 30-day survival was determined by classification and regression tree analysis. Following pooling of data, 240 adults were included; 137 (57.1%) were alive at 30 days. A majority of patients were immunosuppressed (65.8%) and received a ß-lactam (94.6%). Examining the threshold in low-acuity patients (n = 135) to control for co-morbidities, these patients were more likely to survive when fAUC/MIC >12.3 was achieved (63.2% vs. 20.0%; P = 0.015). The difference remained significant in a multivariable logistic regression model that controlled for infection source and immunosuppression (P = 0.017). This threshold is 2-fold lower than that observed with daptomycin monotherapy. Probabilities of threshold attainment using a 10 mg/kg/day dose were 100% for isolates with MICs ≤ 2 mg/L and 95.2% for a 12 mg/kg/day dose for MICs of 4 mg/L. These data support the use of high-dose daptomycin in combination with another antibiotic for treatment of enterococcal bacteraemia.

Antimicrobial Activity of Five Essential Oils against Bacteria and Fungi Responsible for Urinary Tract Infections.

Urinary tract infections are frequently encountered in small animal practice. Escherichia coli and Enterococcus spp. are the most common agents associated to these infections, even though other bacteria and yeasts, such as Candida albicans and Candida famata, may be involved. In view of the increasing problem of the multi-drug resistance, the aim of this study was to investigate the antimicrobial activity of essential oils obtained from star anise (Illicium verum Hook.f.), basil (Ocimum basilicum L.), origanum (Origanum vulgare L.), clary sage (Salvia sclarea L.) and thymus (Thymus vulgaris L.) against multidrug-resistant strains of Escherichia coli, Enterococcus spp., Candida albicans and Candida famata previously isolated from dogs and cats with urinary tract infections. Enterococci were resistant to Illicium verum and Salvia sclarea, such as Candida to Salvia sclarea. Thymus vulgaris and Origanum vulgare essential oils showed the best activity against all the tested pathogens, so they could be proposed for the formulation of external and/or intravesical washes in small animals.

Reduction of bacteria and somatic coliphages in constructed wetlands for the treatment of combined sewer overflow (retention soil filters).

Combined sewer overflows (CSOs) introduce numerous pathogens from fecal contamination, such as bacteria and viruses, into surface waters, thus endangering human health. In Germany, retention soil filters (RSFs) treat CSOs at sensitive discharge points and can contribute to reducing these hygienically relevant microorganisms. In this study, we evaluated the extent of how dry period, series connection and filter layer thickness influence the reduction efficiency of RSFs for Escherichia coli (E. coli), intestinal enterococci (I. E.) and somatic coliphages. To accomplish this, we had four pilot scale RSFs built on a test field at the wastewater treatment plant Aachen-Soers. While two filters were replicates, the other two filters were installed in a series connection. Moreover, one filter had a thinner filtration layer than the other three. Between April 2015 and December 2016, the RSFs were loaded in 37 trials with pre-conditioned CSO after dry periods ranging from 4 to 40 days. During 17 trials, samples for microbial analysis were taken and analyzed. The series connection of two filters showed that the removal increases when two systems with a filter layer of the same height are operated in series. Since the microorganisms are exposed twice to the environmental conditions on the filter surface and in the upper filter layers, there is a greater chance for abiotic adsorption increase. The same effect could be shown when filters with different depths were compared: the removal efficiency increases as filter thickness increases. This study provides new evidence that regardless of seasonal effects and dry period, RSFs can improve hygienic situation significantly.

Frequency and Antibiotic Resistance of Bacteria Implicated in Community Urinary Tract Infections in North Aveiro Between 2011 and 2014.

AIMS: The present study aims to evaluate the predominance of uropathogens responsible for urinary tract infection (UTI) and determine their resistance patterns, to assess if the recommended empirical treatment is appropriate for the studied population. Samples were collected in Aveiro (Portugal) from an ambulatory service between June 2011 and June 2014. RESULTS: From the 4,270 positive urine samples for UTI, 3,561 (83%) were from women and only 709 (17%) were from men. The bacterium Escherichia coli was the most frequent uropathogen, followed by Klebsiella sp., Enterococcus sp., and Proteus mirabilis. E. coli was also the uropathogen presenting less resistance to antibiotics, including those recommended as first and second line UTI treatment. In general, bacteria isolated from men were more resistant to antimicrobials than bacteria isolated from women. CONCLUSIONS: The results of this study emphasized the relevance to consider sex as a differentiating factor in the choice of UTI empirical treatment, mainly due to differences in antimicrobial resistance. From the first line drugs recommended by the European Association of Urology (EAU) to empirical treatment of uncomplicated UTI, nitrofurantoin is the most appropriate drug for both sexes. Ciprofloxacin, although appropriate for treatment in women, is not appropriate to treat UTIs in men. From the second line drugs, both trimethoprim-sulfamethoxazole (TMP-SMX) and amoxicillin-clavulanic acid (AMX-CA) are appropriate drugs for treatment of uncomplicated UTI in women, but not as effective for men.

Dalbavancin in the treatment of different gram-positive infections: a real-life experience.

Dalbavancin is a lipoglycopeptide with a very prolonged half-life enabling treatment with a single intravenous administration that has been approved to treat complicated skin and soft-tissue infections. Information on the efficacy and safety of dalbavancin in other situations is very scarce. This retrospective study included adult patients who received at least one dose of dalbavancin between 2016 and 2017 in 29 institutions in Spain. The primary objective was to report the use of dalbavancin in clinical practice, including its efficacy and tolerability. The potential impact of dalbavancin on reducing the length of hospital stay and hospital costs was also evaluated. A total of 69 patients received dalbavancin during the study period (58.0% male; median age 63.5 years). Dalbavancin was used to treat prosthetic joint infection (29.0%), acute bacterial skin and skin-structure infection (21.7%), osteomyelitis (17.4%) and catheter-related bacteraemia (11.6%). These infections were mainly caused by Staphylococcus aureus (27 isolates), coagulase-negative staphylococci (24 isolates) and Enterococcus spp. (11 isolates). All but two patients received previous antibiotics for a median of 18 days. Dalbavancin was administered for a median of 21 days (range 7-168 days), and concomitant antimicrobial therapy was prescribed to 25 patients (36.2%). The overall clinical success rate of dalbavancin was 84.1%. Adverse events, mainly mild in intensity, were reported in nine patients. Overall, dalbavancin was estimated to reduce hospitalisation by 1160 days, with an estimated overall cost reduction of €211 481 (€3064 per patient). Dalbavancin appears to be an effective therapy for many serious Gram-positive infections.

Antimicrobial resistance of Enterococcus spp. isolated from Thai fermented pork in Chiang Rai Province, Thailand.

OBJECTIVES: The aim of this study was to evaluate the prevalence of antimicrobial-resistant phenotypes and genes of Enterococcus spp. in order to explore the range of resistance profiles from Thai traditional fermented pork. METHODS: A total of 120 Thai fermented pork specimens were collected in Chiang Rai, Thailand. Antimicrobial resistance among isolated enterococci to 11 antimicrobial agents was determined by the agar disk diffusion method. Antibiotic resistance genes from resistant phenotypes and virulence genes were observed. RESULTS: A total of 119 enterococci were found contaminating the collected samples. The most prevalent species was Enterococcus faecalis (68.9%), followed by Enterococcus hirae (16.0%), Enterococcus faecium (13.4%) and Enterococcus gallinarum (1.7%). The highest percentage of resistance was to ciprofloxacin (97.5%), followed by erythromycin (78.2%) and tetracycline (67.2%), whilst high-level gentamicin- and streptomycin-resistant isolates were of lower frequency (7.6% and 22.7%, respectively). All isolates were susceptible to the clinically important agents vancomycin and teicoplanin. Overall, a relatively high frequency of multidrug-resistant (MDR) enterococci was observed (76.2%). Antimicrobial-resistant phenotypes were found to carry aacA-aphD, addE, erm(B), mefA/E, cat, tet(L) and tet(M) resistance genes. Virulence genes were also evaluated and the gelE gene was found to be the most common (37.8%). CONCLUSIONS: These data highlight the importance of MDR enterococci in fermented pork in Thailand. This is the first report to detect the unusual species E. hirae carrying the mefA/E macrolide resistance gene. These clinically important and unusual enterococci isolates from Thai fermented pork could be a source of transferable resistance genes to other bacteria.

A therapeutic benefit of daptomycin against glycopeptide-resistant gram-positive cocci bloodstream infections under neutropenia.

Antibiotic-resistant infections remain to be a major issue for all over the world. Although appropriate diagnosis and rapid treatment initiation are crucially important particularly in immunocompromised patients, selection of antibiotics without identification of causative bacteria is often challenging. A 44-year-old woman with acute myeloid leukemia (AML) under myelosuppression suffered from teicoplanin-resistant gram-positive cocci bacteremia. Taking severe neutropenia due to chemotherapy and glycopeptide-resistance into account, teicoplanin was empirically substituted with daptomycin, which led to prompt defervescence. This microorganism later turned out to be Leuconostoc lactis (L. Lactis), and daptmycin was continued to use based on antimicrobial susceptibility tests. As a result, empiric use of daptomycin successfully controlled glycopeptide-resistant gram-positive cocci bacteremia under neutropenia. This is the first report of daptomycin treatment for L. lactis bacteremia in a patient with AML under neutropenia. Our findings suggest that daptomycin would be a suitable treatment option for glycopeptide-resistant gram-positive cocci bloodstream infections, especially in myelosuppressive patients.

Effects of dietary supplementation with two alternatives to antibiotics on intestinal microbiota of preweaned calves challenged with Escherichia coli K99.

The aim of this study was to investigate the effects of dietary supplementation with two alternatives to antibiotics (Candida tropicalis and mulberry leaf flavonoids) on intestinal microbiota of preweaned calves challenged with Escherichia coli K99. Sixty Holstein calves were randomly assigned to 5 treatments: fed a basal diet (N-CON); fed a basal diet and challenged with E.coli K99 (P-CON); fed a basal diet supplemented with C.tropicalis (CT), mulberry leaf flavonoids (MLF), and the combination of the two additives (CM), respectively, and challenged with E.coli K99. The MLF and CM groups had significantly higher average daily grain and feed efficiency, and significantly lower fecal scores compared with the P-CON group after E. coli K99 challenge. The supplementation groups increased the relative abundance, at the phylum level, of Bacteroidetes and Proteobacteria, whereas at the genus level, they increased the relative abundance of Prevotella, Lactobacillus, and Enterococcus. Quantitative PCR revealed that the CT, MLF, and CM groups had significantly lower copy numbers of E.coli K99 compared with the P-CON group. The CT, MLF, and CM treatments reduce days of diarrhea, improve intestinal health, and beneficially manipulate the intestinal microbiota in preweaned calves.

The role of Enterococcus spp. and multidrug-resistant bacteria causing pyogenic liver abscesses.

BACKGROUND: Pyogenic liver abscesses (PLA) remain a significant clinical problem. Unfortunately, little is known about current bacterial susceptibility profiles and the incidence of multidrug resistant organisms (MDROs) causing PLA in Western countries. Yet, this crucial information is pivotal to guide empirical antibiotic therapy. Aim of this study was to provide detailed characteristics of PLA with a special focus on underlying bacterial pathogens and their susceptibility to antibiotics. METHODS: A retrospective study of patients diagnosed with PLA from 2009 to 2015 in a large tertiary reference center in Germany was performed in order to characterize PLA and antimicrobial susceptibility profiles of causative bacterial species. RESULTS: Overall, 86 patients were included. The most common causes of PLA were bile duct stenosis/obstruction (31.4%) and leakage of biliary anastomosis (15.1%). Frequent predisposing diseases were malignancies (34.9%), diabetes (24.4%) and the presence of liver cirrhosis (16.3%). Of note, Enterococcus spp. were the most frequently cultured bacterial isolates (28.9%), and in 1/3 of cases vancomycin resistance was observed. In addition, a relevant frequency of gram-negative MDROs was identified. In particular, an alarming 10% and 20% of gram-negative bacteria were resistant to carbapenems and tigecycline, respectively. Of note, MDRO status did not predict ICU stay or survival in multivariate regression analysis. The mortality rate in our series was 16.3%. CONCLUSION: Our study demonstrates an as yet underreported role of Enterococcus spp., often associated with vancomycin resistance, as well as of gram-negative MDROs causing PLA.

Metabolic adaptation to the aqueous leaf extract of Moringa oleifera Lam.-supplemented diet is related to the modulation of gut microbiota in mice.

The aqueous leaf extract of Moringa oleifera Lam. (LM-A) is reported to have many health beneficial bioactivities and no obvious toxicity, but have mild adverse effects. Little is known about the mechanism of these reported adverse effects. Notably, there has been no report about the influence of LM-A on intestinal microecology. In this study, animal experiments were performed to explore the relationships between metabolic adaptation to an LM-A-supplemented diet and gut microbiota changes. After 8-week feeding with normal chow diet, the body weight of mice entered a stable period, and one of the group received daily doses of 750-mg/kg body weight LM-A by gavage for 4 weeks (assigned as LM); the other group received the vehicle (assigned as NCD). The liver weight to body weight ratio was enhanced, and the ceca were enlarged in the LM group compared with the NCD group. LM-A-supplemented-diet mice elicited a uniform metabolic adaptation, including slightly influenced fasting glucose and blood lipid profiles, significantly reduced liver triglycerides content, enhanced serum lipopolysaccharide level, activated inflammatory responses in the intestine and liver, compromised gut barrier function, and broken intestinal homeostasis. Many metabolic changes in mice were significantly correlated with altered specific gut bacteria. Changes in Firmicutes, Eubacterium rectale/Clostridium coccoides group, Faecalibacterium prausnitzii, Akkermansia muciniphila, segmented filamentous bacteria, Enterococcus spp., and Sutterella spp. may play an important role in the process of host metabolic adaptation to LM-A administration. Our research provides an explanation of the adverse effects of LM-A administration on normal adult individuals in the perspective of microecology.

Evaluation of Fecal Indicators and Pathogens in a Beef Cattle Feedlot Vegetative Treatment System.

Runoff from open-lot animal feeding areas contains microorganisms that may adversely affect human and animal health if not properly managed. One alternative to full manure containment systems is a vegetative treatment system (VTS) that collects runoff in a sediment basin and then applies it to a perennial vegetation (grass) treatment area that is harvested for hay. Little is known regarding the efficacy of large-scale commercial VTSs for the removal of microbial contaminants. In this study, an active, pump-based VTS designed and built for a 1200-head beef cattle feedlot operation was examined to determine the effects of repeated feedlot runoff application on fecal indicator microorganisms and pathogens over short-term (2 wk) and long-term (3 yr) operations and whether fecal bacteria were infiltrating into deeper soils within the treatment area. In a short-term study, fecal bacteria and pathogen numbers declined over time in soil. Measurements of total coliforms and Enterococcus counts taken on control soils were not effective as fecal indicators. The repeated application of manure-impacted runoff as irrigation water did not enrich the pathogens or fecal indicators in the soil, and no evidence was seen to indicate that pathogens were moving into the deeper soil at this site. These results indicate that large-scale, active VTSs reduce the potential for environmental contamination by manure-associated bacteria. Also, this study has implications to full-containment systems that apply runoff water to land application areas (cropland) and the fate of pathogens in the soils of land application sites.

Etiologies of community-onset urinary tract infections requiring hospitalization and antimicrobial susceptibilities of causative microorganisms.

BACKGROUND: Community-onset urinary tract infections (CoUTIs) are the most common bacterial infections, and a decline in antibiotic susceptibility causes many clinical challenges. Adequate empiric antibiotic treatment can decrease unnecessary hospital stays and complications, while reducing the antimicrobial resistance progression. METHODS: From October 2014 to April 2015, we retrospectively enrolled patients who were at least 18 years old and required hospitalization for CoUTIs. Demographic variables of these patients, and uropathogens and their antimicrobial susceptibilities were evaluated. RESULTS: In total, 457 patients were enrolled in this study. Their mean age was 71.9 years, and 35.2% of the patients were male. Escherichia coli (54.5%) was the most common uropathogen, followed by Klebsiella pneumoniae (13.1%), Enterococcus spp. (7.1%), Pseudomonas aeruginosa (4.6%), and Proteus mirabilis (3.5%). Bacteremia was present in 25.2% of patients. Diabetes mellitus and acute kidney injury at admission were risk factors for CoUTIs with concomitant bacteremia. Among the UTI-associated bloodstream strains, E. coli (53.1%) was also the most predominant pathogen, followed by K. pneumoniae (11.3%), Staphylococcus aureus (6.1%), and P. mirabilis (4.3%). The overall susceptibility of cefazolin was 62.8%, ceftriaxone 71.4%, ceftazidime 82.8%, flomoxef 82%, cefepime 94.5%, ampicillin-sulbactam 41.6%, piperacillin-tazobactam 85%, levofloxacin 65.2%, trimethoprim-sulfamethoxazole 61.5%, imipenem 92.3%, gentamicin 76.1%, and amikacin 97.5%. Cefazolin-susceptible isolates could be found more frequently among patients who are less than 65 years of age and without diabetes mellitus, had no UTI episode in the past year, and have no bacteremia risk. Patients with nasogastric tube retention more commonly experienced antimicrobial resistance to all the third-generation cephalosporins. CONCLUSION: Third-generation cephalosporins effectively treated CoUTIs. However, patients with nasogastric tube retention more commonly experienced cephalosporin resistance. Cefepime, imipenem, and amikacin may be used in patients with higher antimicrobial resistance. In selected patients, cefazolin may still be an adequate drug of choice for CoUTIs.