Recovery of nosocomial fecal flora from frozen stool specimens and rectal swabs: comparison of preservatives for epidemiological studies

Effect of cryopreservation medium conditions on growth and isolation of gut anaerobes from human faecal samples

BACKGROUND

Novel strategies for anaerobic bacterial isolations from human faecal samples and various initiatives to generate culture collections of gut-derived bacteria have instigated considerable interest for the development of novel microbiota-based treatments. Early in the process of building a culture collection, optimal faecal sample preservation is essential to safeguard the viability of the broadest taxonomic diversity range possible. In contrast to the much more established faecal storage conditions for meta-omics applications, the impact of stool sample preservation conditions on bacterial growth recovery and isolation remains largely unexplored. In this study, aliquoted faecal samples from eleven healthy human volunteers selected based on a range of physicochemical and microbiological gradients were cryopreserved at - 80 °C either without the addition of any medium (dry condition) or in different Cary-Blair medium conditions with or without a cryoprotectant, i.e. 20% (v/v) glycerol or 5% (v/v) DMSO. Faecal aliquots were subjected to bulk 16S rRNA gene sequencing as well as dilution plating on modified Gifu Anaerobic Medium after preservation for culturable fraction profiling and generation of bacterial culture collections.

RESULTS

Analyses of compositional variation showed that cryopreservation medium conditions affected quantitative recovery but not the overall community composition of cultured fractions. Post-preservation sample dilution and richness of the uncultured source samples were the major drivers of the cultured fraction richness at genus level. However, preservation conditions differentially affected recovery of specific genera. Presence-absence analysis indicated that twenty-two of the 45 most abundant common genera (>0.01% abundance, dilution 10^-4) were recovered in cultured fractions from all preservation conditions, while nine genera were only detected in fractions from a single preservation condition. Overall, the highest number of common genera (i.e. 35/45) in cultured fractions were recovered from sample aliquots preserved without medium and in the presence of Cary-Blair medium containing 5% (v/v) DMSO. Also, in the culture collection generated from the cultured fractions, these two preservation conditions yielded the highest species richness (72 and 66, respectively).

CONCLUSION

Our results demonstrate that preservation methods partly determine richness and taxonomic diversity of gut anaerobes recovered from faecal samples. Complementing the current standard practice of cryopreserving stool samples in dry conditions with other preservation conditions, such as Cary-Blair medium with DMSO, could increase the species diversity of gut-associated culture collections. Video abstract.

The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli

Investigators often rely on studies of Escherichia coli to characterize the burden of antibiotic resistance in a clinical or community setting. To determine if prevalence estimates for antibiotic resistance are sensitive to sample handling and interpretive criteria, we collected presumptive E. coli isolates (24 or 95 per stool sample) from a community in an urban informal settlement in Kenya. Isolates were tested for susceptibility to nine antibiotics using agar breakpoint assays and results were analyzed using generalized linear mixed models. We observed a <3-fold difference between prevalence estimates based on freshly isolated bacteria when compared to isolates collected from unprocessed fecal samples or fecal slurries that had been stored at 4°C for up to 7days. No time-dependence was evident (P>0.1). Prevalence estimates did not differ for five distinct E. coli colony morphologies on MacConkey agar plates (P>0.2). Successive re-plating of samples for up to five consecutive days had little to no impact on prevalence estimates. Finally, culturing E. coli under different conditions (with 5% CO₂ or micro-aerobic) did not affect estimates of prevalence. For the conditions tested in these experiments, minor modifications in sample processing protocols are unlikely to bias estimates of the prevalence of antibiotic-resistance for fecal E. coli.

Faecal microbiota transplant for recurrent Clostridium difficile infection using long-term frozen stool is effective: clinical efficacy and bacterial viability data

BACKGROUND

Faecal microbial transplant (FMT) for recurrent Clostridium difficile infection (rCDI) is greatly facilitated by frozen stool banks. However, the effect of frozen storage of stool for greater than 2 months on the viability of stool bacteria is unknown and the efficacy of FMT is not clear.

AIM

To evaluate the viability of bacteria in stool frozen for up to 6 months, and the clinical efficacy of FMT with stool frozen for 2-10 months, for the treatment of rCDI.

METHODS

Viability of six representative groups of faecal bacteria after 2 and 6 months of storage at -80 °C, in normal saline (NS) or 10% glycerol were assessed by culture on plate media. The clinical outcomes of 16 consecutive patients with rCDI treated with aliquots of stool frozen in 10% glycerol and stored for 2-10 months were also examined.

RESULTS

Viability at both 2 and 6 months was similar to baseline, in specimens stored in 10% glycerol and at 2 months in stool stored in NS, but was reduced by >1 log at 6 months for Aerobes (P < 0.01), total Coliforms (P < 0.01) and Lactobacilli (P < 0.01) in NS. Using stool frozen for 2-10 months in 10% glycerol, the cure rate for rCDI was 88% with one FMT and 100% after repeat FMT in those who relapsed.

CONCLUSION

Stool for faecal microbial transplant to treat rCDI can be safely stored frozen in 10% glycerol for at least 6 months without loss of clinical efficacy or viability in the six bacterial groups tested.

Duration of colonization with antimicrobial-resistant bacteria after ICU discharge

PURPOSE

Readmission of patients colonized with antimicrobial-resistant bacteria (AMRB) is important in the nosocomial dynamics of AMRB. We assessed the duration of colonization after discharge from the intensive care unit (ICU) with highly resistant Enterobacteriaceae (HRE), methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE).

METHODS

Data were obtained from a cluster-randomized trial in 13 ICUs in 8 European countries (MOSAR-ICU trial, 2008-2011). All patients were screened on admission and twice weekly for AMRB. All patients colonized with HRE, MRSA, or VRE and readmitted to the same ICU during the study period were included in the current analysis. Time between discharge and readmission was calculated, and the colonization status at readmission was assessed. Because of interval-censored data, a maximum likelihood analysis was used to calculate the survival function, taking censoring into account. A nonparametric two-sample test was used to test for differences in the survival curves.

RESULTS

The MOSAR-ICU trial included 14,390 patients, and a total of 64,997 cultures were taken from 8,974 patients admitted for at least 3 days. One hundred twenty-five unique patients had 141 episodes with AMRB colonization and at least 1 readmission. Thirty-two patients were colonized with two or more AMRBs. Median times until clearance were 4.8 months for all AMRB together, 1.4 months for HRE, <1 month for MRSA, and 1.5 months for VRE. There were no significant differences between the survival curves.

CONCLUSION

Fifty percent of the patients had lost colonization when readmitted 2 or more months after previous ICU discharge.

Recovery of antimicrobial-resistantEscherichia coliafter storage of bovine feces in Cary–Blair medium

The effect of storing bovine feces in Cary–Blair medium on the recovery of antimicrobial-resistant Escherichia coli was investigated. Feces from cattle at a research feedlot (n = 50) and at a commercial feedlot (n = 46) were processed immediately or after storage in Cary–Blair medium for 8 days at 5 °C. Total, ampicillin-resistant, and tetracycline-resistant E. coli were isolated. The number of total E. coli decreased slightly after storage (0.19 log units; p < 0.001), but storage of feces in Cary–Blair medium did not affect recovery of ampicillin- or tetracycline-resistant E. coli.

Efficient recovery of fluoroquinolone-susceptible and fluoroquinolone-resistant Escherichia coli strains from frozen samples

We assessed the rate of recovery of fluoroquinolone-resistant and fluoroquinolone-susceptible Escherichia coli isolates from culture of frozen perirectal swab samples compared with the results for culture of the same specimen before freezing. Recovery rates for these 2 classes of E. coli were 91% and 83%, respectively. The majority of distinct strains recovered from the initial sample were also recovered from the frozen sample. The strains that were not recovered were typically present only in low numbers in the initial sample. These findings emphasize the utility of frozen surveillance samples.

Bacterial metabolism and health-related effects of galacto-oligosaccharides and other prebiotics

Most studies involving prebiotic oligosaccharides have been carried out using inulin and its fructo-oligosaccharide (FOS) derivatives, together with various forms of galacto-oligosaccharides (GOS). Although many intestinal bacteria are able to grow on these carbohydrates, most investigations have demonstrated that the growth of bifidobacteria, and to a lesser degree lactobacilli, is particularly favoured. Because of their safety, stability, organoleptic properties, resistance to digestion in the upper bowel and fermentability in the colon, as well as their abilities to promote the growth of beneficial bacteria in the gut, these prebiotics are being increasingly incorporated into the Western diet. Inulin-derived oligosaccharides and GOS are mildly laxative, but can result in flatulence and osmotic diarrhoea if taken in large amounts. However, their effects on large bowel habit are relatively minor. Although the literature dealing with the health significance of prebiotics is not as extensive as that concerning probiotics, considerable evidence has accrued showing that consumption of GOS and FOS can have significant health benefits, particularly in relation to their putative anti-cancer properties, influence on mineral absorption, lipid metabolism, and anti-inflammatory and other immune effects such as atopic disease. In many instances, prebiotics seem to be more effective when used as part of a synbiotic combination.

Colonization and resistance dynamics of gram-negative bacteria in patients during and after hospitalization

The colonization and resistance dynamics of aerobic gram-negative bacteria in the intestinal and oropharyngeal microfloras of patients admitted to intensive care units (ICU) and general wards were investigated during and after hospitalization. A total of 3,316 specimens were obtained from patients upon admission, once weekly during hospitalization, at discharge from the ICU, at discharge from the hospital, and 1 and 3 months after discharge from the hospital. Five colonies per specimen were selected for identification and susceptibility testing. In both patient populations, the gram-negative colonization rates in oropharyngeal specimens increased during hospitalization and did not decrease in the 3 months after discharge. In rectal specimens, colonization rates decreased during hospitalization and increased after discharge. There was a change in species distribution among the dominant microfloras during hospitalization. Klebsiella spp., Enterobacter spp., Serratia marcescens, and Pseudomonas aeruginosa were isolated more often, whereas the frequency of Escherichia coli declined. The percentage of ICU patients colonized with ampicillin- and/or cephalothin-resistant fecal E. coli was significantly increased at discharge from the hospital and did not change in the 3 months after discharge. The emergence of multidrug resistance was observed for E. coli during patient stays in the ICU. Resistance frequencies in E. coli significantly increased with the length of stay in the ICU. For the general ward population, no significant changes in resistance frequencies were found during hospitalization. From a population perspective, the risk of dissemination of resistant gram-negative bacteria into the community through hospitalized patients appears to be low for general ward patients but is noticeably higher among ICU patients.

High rate of false-negative results of the rectal swab culture method in detection of gastrointestinal colonization with vancomycin-resistant enterococci

The diagnostic accuracy of the rectal swab (RS) culture method in identifying gastrointestinal colonization with vancomycin-resistant enterococci (VRE) is not known. Serial quantitative stool cultures, skin cultures, and RS cultures were performed for patients with VRE infections to assess the false-negative rate of the RS and the prevalence of skin colonization, a prerequisite for cross-transmission, at varying VRE stool densities. A total of 35 stool samples were obtained from 13 patients. The sensitivity of the RS culture was 58%; it ranged from 100%, at VRE densities of > or =7.5 log10 colony forming units (cfu) per gram of stool, to 0%, at densities of < or =4.5 log10 cfu per gram of stool. Skin colonization was detected at these low VRE stool densities, but it was more common at higher VRE densities (P<.001). Antibiotic exposure was significantly associated with higher VRE stool densities (P<.001). The high false-negative rate of the RS may be contributing to the continued increase in the prevalence of VRE.