Fecal microbiota transplantation against intestinal colonization by extended spectrum beta-lactamase producing Enterobacteriaceae: a proof of principle study.
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ABSTRACT:
SUBMITTER: Singh R
PROVIDER: S-EPMC5863815 | biostudies-literature | 2018 Mar
REPOSITORIES: biostudies-literature
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Project description:Extended-spectrum ?-lactamase-producing Enterobacteriaceae (EPE) are a major cause of bloodstream infections, and the colonization rate of EPE in the gut microbiota of individuals lacking prior hospitalization or comorbidities is increasing. In this study, we performed an in-depth investigation of the temporal dynamics of EPE and their plasmids during one year by collecting fecal samples from three patients initially seeking medical care for urinary tract infections. In two of the patients, the same strain that caused the urinary tract infection (UTI) was found at all consecutive samplings from the gut microbiota, and no other EPEs were detected, while in the third patient the UTI strain was only found in the initial UTI sample. Instead, this patient presented a complex situation where a mixed microbiota of different EPE strain types, including three different E. coli ST131 variants, as well as different bacterial species, was identified over the course of the study. Different plasmid dynamics were displayed in each of the patients, including the spread of plasmids between different strain types over time and the transposition of bla CTX-M-15 from the chromosome to a plasmid, followed by subsequent loss through homologous recombination. Small cryptic plasmids were found in all isolates from all patients, and they appear to move frequently between different strains in the microbiota. In conclusion, we could demonstrate an extensive variation of EPE strain types, plasmid composition, rearrangements, and horizontal gene transfer of genetic material illustrating the high dynamics nature and interactive environment of the gut microbiota during post-UTI carriage.
| S-EPMC6437490 | biostudies-literature
Project description:Extended Spectrum Beta-Lactamase-producing Enterobacteriaceae Raw sequence reads
| PRJNA476828 | ENA
Project description:Organisms producing extended-spectrum beta-lactamases (ESBLs) have been reported in many countries, but there is no information on the prevalence of ESBL-producing members of the family Enterobacteriaceae in Cameroon. A total of 259 Enterobacteriaceae strains were isolated between 1995 and 1998 from patients at the Yaounde Central Hospital in Cameroon. Enterobacterial isolates resistant to extended-spectrum cephalosporin and monobactam were screened for ESBL production by the double-disk (DD) synergy test. Thirty-one (12%) of these Enterobacteriaceae strains were shown to be positive by the DD synergy test, suggesting the presence of ESBLs. Resistance to oxyimino-cephalosporins and monobactams of 12 (38.7%) of the 31 strains-i.e., 6 Klebsiella pneumoniae, 4 Escherichia coli, 1 Citrobacter freundii, and 1 Enterobacter cloacae strain-was transferred to E. coli HK-225 by conjugation. Resistance to gentamicin, gentamicin plus trimethoprim-sulfamethoxazole, or trimethoprim-sulfamethoxazole was cotransferred into 6, 2, and 1 of these transconjugants, respectively. All 12 transconjugants were resistant to amoxicillin, piperacillin, all of the cephalosporins, and aztreonam but remained susceptible to cefoxitin and imipenem. Crude extracts of beta-lactamase-producing transconjugants were able to reduce the diameters of inhibition zones around disks containing penicillins, narrow- to expanded-spectrum cephalosporins or monobactams when tested against a fully susceptible E. coli strain but had no effect on such zones around cefoxitin, imipenem, and amoxicillin-clavulanate disks. The beta-lactamases produced by the 12 tranconjugants turned out to be SHV-12 by DNA sequencing. Therefore, the ESBL SHV-12 is described for the first time in Cameroon.
| S-EPMC1169189 | biostudies-literature
Project description:Extended-spectrum-?-lactamase (ESBL)/AmpC producing Enterobacteriaceae have been reported worldwide amongst isolates obtained from humans, food-producing animals, companion animals, and environmental sources. However, data on prevalence of fecal carriage of ESBL/AmpC producing Enterobacteriaceae in healthy companion animals is limited. This pilot study describes the prevalence of ESBL/AmpC encoding genes in healthy cats and dogs, and cats and dogs with diarrhea. Twenty fecal samples of each group were cultured on MacConkey agar supplemented with 1 mg/L cefotaxime and in LB-enrichment broth supplemented with 1 mg/L cefotaxime, which was subsequently inoculated on MacConkey agar supplemented with 1 mg/L cefotaxime. ESBL/AmpC genes were identified using the Check-Points CT103 micro array kit and subsequently by sequencing analysis. Chromosomal ampC promoter mutations were detected by PCR and sequencing analysis. From the healthy and diarrheic dogs, respectively 45 and 55% were positive for Escherichia coli with reduced susceptibility for cefotaxime. From the healthy and diarrheic cats, the estimated prevalence was respectively 0 and 25%. One diarrheic cat was positive for both reduced susceptible E. coli and Proteus mirabilis. The ESBL/AmpC genes found in this study were mainly bla CTX-M-1, but also bla CTX-M-14, bla CTX-M-15, bla TEM-52-StPaul, bla SHV-12, and bla CMY-2 were detected. This pilot study showed that the prevalence of ESBL/AmpC producing Enterobacteriaceae in healthy and diarrheic dogs, and diarrheic cats was relatively high. Furthermore, the genes found were similar to those found in isolates of both human and food-producing animal origin. However, since the size of this study was relatively small, extrapolation of the data to the general population of cats and dogs should be done with great care.
| S-EPMC3745002 | biostudies-literature
Project description:Fresh vegetables are an essential part of a healthy diet, but microbial contamination of fruits and vegetables is a serious concern to human health, not only for the presence of foodborne pathogens but because they can be a vehicle for the transmission of antibiotic-resistant bacteria. This work aimed to investigate the importance of fresh produce in the transmission of extended-spectrum β-lactamases (ESBL)-producing Enterobacteriaceae. A total of 174 samples of vegetables (117) and farm environment (57) were analysed to determine enterobacterial contamination and presence of ESBL-producing Enterobacteriaceae. Enterobacterial counts above the detection limit were found in 82.9% vegetable samples and 36.8% environmental samples. The average count was 4.2 log cfu/g or mL, with a maximum value of 6.2 log cfu/g in a parsley sample. Leafy vegetables showed statistically significant higher mean counts than other vegetables. A total of 15 ESBL-producing isolates were obtained from vegetables (14) and water (1) samples and were identified as Serratia fonticola (11) and Rahnella aquatilis (4). Five isolates of S. fonticola were considered multi-drug resistant. Even though their implication in human infections is rare, they can become an environmental reservoir of antibiotic-resistance genes that can be further disseminated along the food chain.
| S-EPMC8619215 | biostudies-literature
Project description:A prospective cohort study was performed among travelers from the Netherlands to investigate the acquisition of carbapenemase-producing Enterobacteriaceae (CP-E) and extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) and associated risk factors. Questionnaires were administered and rectal swab samples were collected and tested before and after traveler return. Of 370 travelers, 32 (8.6%) were colonized with ESBL-E before trave,; 113 (30.5%) acquired an ESBL-E during travel, and 26 were still colonized 6 months after return. No CP-E were found. Independent risk factors for ESBL-E acquisition were travel to South and East Asia. Multilocus sequence typing showed extensive genetic diversity among Escherichia coli. Predominant ESBLs were CTX-M enzymes. The acquisition rate, 30.5%, of ESBL-E in travelers from the Netherlands to all destinations studied was high. Active surveillance for ESBL-E and CP-E and contact isolation precautions may be recommended at admission to medical facilities for patients who traveled to Asia during the previous 6 months.
| S-EPMC3739527 | biostudies-literature
Project description:Molecular typing has become indispensable in the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings, but current methods are labor-intensive, are difficult to standardize, or have limited resolution. Whole-genome multilocus sequence typing (wgMLST) has emerged as a whole-genome sequencing (WGS)-based gene-by-gene typing method that may overcome these limitations and has been applied successfully for several species in outbreak settings. In this study, genus-, genetic-complex-, and species-specific wgMLST schemes were developed for Citrobacter spp., the Enterobacter cloacae complex, Escherichia coli, Klebsiella oxytoca, and Klebsiella pneumoniae and used to type a national collection of 1,798 extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) isolates obtained from patients in Dutch hospitals. Genus-, genetic-complex-, and species-specific thresholds for genetic distance that accurately distinguish between epidemiologically related and unrelated isolates were defined for Citrobacter spp., the E. cloacae complex, E. coli, and K. pneumoniae wgMLST was shown to have higher discriminatory power and typeability than in silico MLST. In conclusion, the wgMLST schemes developed in this study facilitate high-resolution WGS-based typing of the most prevalent ESBL-producing species in clinical practice and may contribute to further elucidation of the complex epidemiology of antimicrobial-resistant Enterobacteriaceae wgMLST opens up possibilities for the creation of a Web-accessible database for the global surveillance of ESBL-producing bacterial clones.
| S-EPMC5121380 | biostudies-literature
Project description:Background: We aimed to investigate the prevalence, molecular epidemiology and prevalence factors for Extended Spectrum ?-Lactamase-producing Enterobacteriaceae (ESBL-E) shedding by race horses. A cross-sectional study was performed involving fecal samples collected from 169 Thoroughbred horses that were housed at a large racing facility in Ontario, Canada. Samples were enriched, plated on selective plates, sub-cultured to obtain pure cultures and ESBL production was confirmed. Bacterial species were identified and antibiotic susceptibility profiles were assessed. E. coli sequence types (ST) and ESBL genes were determined using multilocus sequence type (MLST) and sequencing. Whole genome sequencing was performed to isolates harboring CTX-M-1 gene. Medical records were reviewed and associations were investigated.Results: Adult horses (n?=?169), originating from 16 different barns, were sampled. ESBL-E shedding rate was 12% (n?=?21/169, 95% CI 8-18%); 22 ESBL-E isolates were molecularly studied (one horse had two isolates). The main species was E. coli (91%) and the major ESBL gene was CTX-M-1 (54.5%). Ten different E. coli STs were identified. Sixty-four percent of total isolates were defined as multi-drug resistant. ESBL-E shedding horses originated from 8/16 different barns; whereas 48% (10/21) of them originated from one specific barn. Overall, antibiotic treatment in the previous month was found as a prevalence factor for ESBL-E shedding (p?=?0.016, prevalence OR?=?27.72, 95% CI 1.845-416.555).Conclusions: Our findings demonstrate the potential diverse reservoir of ESBL-E in Thoroughbred race horses. Multi-drug resistant bacteria should be further investigated to improve antibiotic treatment regimens and equine welfare.
| S-EPMC7726890 | biostudies-literature
Project description:In this study, we characterized the ?-lactamase genes and phenotypic resistance of cephalosporin-resistant Enterobacteriaceae isolated from retail foods in China. Of 1,024 Enterobacteriaceae isolates recovered from raw meat products, aquatic products, raw vegetables, retail-level ready-to-eat (RTE) foods, frozen foods, and mushrooms from 2011 to 2014, 164 (16.0%) showed cefotaxime (CTX) and/or ceftazidime (CAZ) cephalosporin resistance, and 96 (9.4%) showed the extended-spectrum ?-lactamase (ESBL) phenotype. More than 30% isolates were resistant to all antimicrobial agents except carbapenems (MEM 3.1% and IPM 5.2%), cefoxitin (FOX 6.3%), and amoxicillin/clavulanic acid (AMC 26%), and 94.8% of the strains were resistant to up to seven antibiotics. Polymerase chain reaction analysis showed that blaTEM (81.9%) was the most common gene, followed by blaCTX-M (68.1%) and blaSHV (38.9%). Moreover, 16.8% (72/429) of food samples contained ESBL-positive Enterobacteriaceae, with the following patterns: 32.9% (23/70) in frozen foods, 27.2% (5/29) in mushrooms, 17.6% (24/131) in raw meats, 13.3% (4/30) in fresh vegetables, 11.1% (8/72) in RTE foods, and 9.3% (9/97) in aquatic products. In addition, 24 of 217 foods collected in South China (11.1%), 25 of 131 foods collected in North of the Yangtze River region (19.1%), and 23 of 81 foods collected in South of the Yangtze River region (28.4%) were positive for ESBL- Enterobacteriaceae. Conjugation experiments demonstrated that the 22 of 72 isolates were transconjugants that had received the ?-lactamase gene and were resistant to ?-lactam antibiotics as well as some non-?-lactam antibiotics. These findings demonstrated that retail foods may be reservoirs for the dissemination of ?-lactam antibiotics and that resistance genes could be transmitted to humans through the food chain; and the predominant ESBL-producing Enterobacteriaceae in China was isolated from in frozen chicken-meat, followed by frozen pork, cold noodles in sauce, cucumber, raw chicken meat, frozen pasta, brine-soaked chicken and tomato.
| S-EPMC6092486 | biostudies-literature
Project description:BackgroundBacteremia caused by extended-spectrum ?-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) is associated with inadequate empirical therapy and substantial mortality in neutropenic patients. Strategies are needed to identify neutropenic patients at high risk of these infections.MethodsFrom April 2014 to September 2016, we collected perianal swabs, both at admission and weekly thereafter, from patients undergoing hematopoietic stem cell transplantation (HSCT). Patients received prophylactic levofloxacin while neutropenic. Swabs were plated onto selective agar, colonies were identified and underwent antimicrobial susceptibility testing, and phenotypic ESBL testing and polymerase chain reaction for ?-lactamase genes were performed on ceftriaxone-resistant Enterobacteriaceae. We then determined the prevalence of pre-transplant ESBL-E colonization and risk of ESBL-E bacteremia. Colonizing and bloodstream isolates from patients with ESBL-E bacteremia underwent multilocus sequence typing and pulsed-field gel electrophoresis.ResultsWe analyzed 312 patients, including 212 allogeneic and 100 autologous HSCT recipients. Ten percent (31/312) of patients had pre-transplant ESBL-E colonization. Susceptibility rates of colonizing ESBL-E were: levofloxacin, 25%; cefepime, 9%; piperacillin-tazobactam, 84%; and meropenem, 97%. Of 31 patients colonized with ESBL-E pre-transplant, 10 (32%) developed ESBL-E bacteremia during their transplant admission, compared to 1 (0.4%) of 281 patients not colonized with ESBL-E (P < .001). All bloodstream ESBL-E were levofloxacin-resistant and colonizing and bloodstream isolates from individual patients had identical genotypic profiles.ConclusionsHSCT recipients who are colonized with levofloxacin-resistant ESBL-E pre-transplant and receive levofloxacin prophylaxis have high rates of bacteremia from their colonizing strain during neutropenia. Assessing for ESBL-E colonization in neutropenic patients could lead to optimization of empirical antibacterial therapy.
| S-EPMC6233682 | biostudies-literature