We utilized high-throughput sequencing to analyse the effects of vancomycin on the faecal human microbiota up to 22 weeks post-antibiotic cessation.
The clinical relevance of the observed microbiota perturbations was studied in mice. During vancomycin therapy, most intestinal microbiota genera and operational taxonomic units OTUs were depleted in all analysed subjects, including all baseline OTUs from the phylum Bacteroidetes.
Following antibiotic cessation, marked differences in microbiota resilience were observed among subjects. The clinical relevance of the observed microbiota changes was further demonstrated in mice, which developed analogous microbiota alterations.
During vancomycin treatment, mice were highly susceptible to intestinal colonization by an antibiotic-resistant pathogen and, upon antibiotic cessation, a less-resilient microbiota allowed higher levels of pathogen colonization. Oral vancomycin induces drastic and consistent changes in the human intestinal microbiota.
Upon vancomycin cessation, the microbiota recovery rate varied considerably among subjects, which could influence, as validated in mice, the level of susceptibility to pathogen intestinal colonization.
Our results demonstrate the negative long-term effects of vancomycin, which should be considered as a fundamental aspect of the cost—benefit equation for antibiotic prescription.
The intestinal microbiota is essential for the proper development of the intestinal tract and maturation of the immune and nervous system. In addition, commensal bacteria confer resistance to infection by suppressing the growth of intestinal pathogens. Vancomycin, a glycopeptide antibiotic mainly active against Gram-positive bacteria, is often used to treat infections produced by multidrug-resistant Staphylococcus aureus and Clostridium difficile. Indeed, among the different antibiotics currently available, oral vancomycin remains the treatment of choice for severe C.
Despite the potential negative effects caused by vancomycin administration, the impact that this antibiotic has on the human microbiota is not well characterized. Indeed, most prior studies analysing intestinal microbiota changes upon vancomycin administration have focused on CDI patients.
Moreover, subjects recruited for these studies were only followed for up to one month after antibiotic discontinuation, rendering the long-lasting effects of vancomycin unknown. In addition, these reports have only partially characterized the changes in the microbiota upon vancomycin administration. Indeed, only changes at the family level, 16 or changes in particular bacterial groups have been defined. To better characterize the effects of vancomycin on the intestinal microbiota, we have analysed, using 16S rRNA high-throughput sequencing, the faecal microbiota of patients with treatment-naive, new-onset rheumatoid arthritis RA who underwent a 2 week course of oral vancomycin.
These patients had not been exposed to any other antibiotic at least 3 months prior to vancomycin administration, nor were they exposed to immunosuppressive therapies, allowing us to clearly define the microbiota changes solely produced by this antibiotic. Further details are published on the www. All included patients gave their consent to participate in the study. All RA patients were recruited from a previously described study. After consent was obtained, we randomly divided new-onset RA patients into two groups.
The first group the vancomycin-treated group received vancomycin orally mg four times a day for 2 weeks, followed by treatment with methotrexate starting 6 weeks after discontinuation of antibiotic therapy. The second group control group received methotrexate from the beginning of the study and did not receive vancomycin.
This control group was included to identify changes in the microbiota due to methotrexate administration. Importantly, as described below, no alterations in the gut microbiota composition were observed at any studied timepoint in the control group. Bacterial DNA extraction, amplification of 16S rRNA gene and high-throughput sequencing analysis, including confirmation of the obtained results using different subset of sequences, are indicated in the supplementary methods and Figures S7—S10 available as Supplementary data at JAC Online.
The two-tailed Student's t -test was applied to identify significant differences in the number of operational taxonomic units OTUs , genera or Shannon index. The two-tailed Wilcoxon non-parametric test was applied to identify significant microbiota taxonomic changes that occur in patients after vancomycin therapy.
The false discovery rate FDR approach was applied to adjust for multiple hypothesis testing. Correlation between the microbiota recovery rate and susceptibility to intestinal colonization by VRE were analysed using the Spearman test. Details on the mouse experimental procedures are described in the supplementary methods. Twenty-one subjects were included in the study. Nine of the patients received vancomycin orally for 2 weeks, followed by methotrexate beginning 6 weeks after vancomycin cessation , while 12 subjects were only treated with oral methotrexate from day 1 control group; no vancomycin.
No significant differences in clinical or demographic baseline characteristics were observed between both groups Table S1, available as Supplementary data at JAC Online. Faecal samples were obtained immediately before the initiation of vancomycin treatment, the day the treatment was ended week 2 , and 2, 6, 14 and 22 weeks after antibiotic discontinuation.
Samples from control patients were obtained at the same timepoints. With only a few exceptions, samples for most timepoints were included in the study for all vancomycin-treated 4. First, to obtain a global view of the changes induced by vancomycin, we applied hierarchical clustering see the supplementary methods to group samples by microbiota similarity samples with a more similar microbiota will be those grouped together in the same branch of the tree. As shown in Figure 1 a , oral methotrexate alone did not produce major changes in the faecal microbiota, as all prospective samples from control patients cluster with their respective baseline samples.
In contrast, oral administration of vancomycin for 2 weeks consistently altered the faecal microbiota structure, with all faecal samples obtained immediately after vancomycin treatment clustering together and away from their respective baseline samples. After antibiotic cessation, a few vancomycin-treated patients recovered their overall baseline microbiota structure i.
However, the faecal microbiota structure for most vancomycin-treated patients remained altered, even 22 weeks after antibiotic cessation i. Vancomycin induces persistent changes in the structure and richness of the human microbiota. Patients received vancomycin treatment for 2 weeks T, vancomycin treated or did not receive vancomycin C, control group.
Faecal samples were obtained immediately before treatment Baseline , the day of antibiotic cessation Vanco , and 2, 6, 14 and 22 weeks w after antibiotic cessation Recovery. As control, faecal samples from patients that did not receive vancomycin were obtained at similar timepoints. Samples with a more similar microbiota are clustered within the same branch of the tree. Colours indicate the time frame where the faecal sample was obtained.
Numbers indicate the patient ID. Those samples obtained at the last timepoint 22 weeks post-antibiotic withdrawal are labelled with asterisks. For comparison, the same indices were calculated from the faecal samples collected at similar timepoints from patients who did not receive vancomycin control. Subsequently, we analysed the impact of vancomycin treatment on microbiota richness, measured as the number of identified OTUs, a sequencing approach that closely defines the number of bacterial species within a sample.
The number of OTUs did not differ over time in the control patients not receiving vancomycin Figure 1 b and Figure S2. By contrast, microbiota richness was greatly reduced upon vancomycin administration. Following antibiotic cessation, microbiota richness gradually increased, although it never recovered to baseline levels. A similar result was obtained when the Shannon diversity index was calculated Figure 1 c and Figure S3 , which takes into account the number of OTUs and their relative proportion.
In this case, however, baseline levels were recovered 22 weeks after antibiotic withdrawal. Considering the large effects of vancomycin on the overall microbiota structure and richness, we next decided to examine its effects on specific taxa. Vancomycin treatment greatly reduced the levels of the Bacteroidetes phylum Figure 2 a. In contrast, the Proteobacteria and Fusobacteria phyla underwent a drastic expansion after vancomycin therapy.
The abundance of most analysed genera and OTUs was also significantly altered by vancomycin treatment Figure 2 b and c. Indeed, most abundant genera and OTUs from the Bacteroidetes or Firmicutes phyla could not be detected in any of the patients after vancomycin treatment. Nonetheless, some Firmicutes increased after vancomycin treatment i.
Megasphaera , Veillonella , likely explaining why, overall, the Firmicutes phylum did not diminish upon vancomycin treatment Figure 2 a. Importantly, several genera belonging to the Proteobacteria phylum i. The abundance of the majority of taxa and OTUs is altered during vancomycin treatment. Genera are sorted by phyla, FC difference and then alphabetically. UC, unclassified; vanco, vancomycin. We next examined the capacity of the different commensal bacteria to recover after antibiotic cessation.
We focused on those commensals whose relative abundance significantly changed during vancomycin therapy. As shown in Figure 3 , the speed of recovery was different depending on the phyla, genera or OTU analysed. Nevertheless, 22 weeks post-antibiotic cessation, all genera and phyla had recovered their baseline levels with the exception of only two OTUs which still showed significant alterations.
Changes in the human microbiota following vancomycin withdrawal. Time 0 represents the sample obtained the day of vancomycin withdrawal. UC, unclassified; Enterobact. All rights reserved. Information is for End User's use only and may not be sold, redistributed or otherwise used for commercial purposes. Mayo Clinic does not endorse companies or products. Advertising revenue supports our not-for-profit mission.
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Please try again. Something went wrong on our side, please try again. For non-prescription products, read the label or package ingredients carefully. Appropriate studies performed to date have not demonstrated pediatric-specific problems that would limit the usefulness of vancomycin injection in children.
Appropriate studies performed to date have not demonstrated geriatric-specific problems that would limit the usefulness of vancomycin injection in the elderly. However, elderly patients are more likely to have hearing, kidney, or heart problems, which may require caution and an adjustment in the dose for patients receiving this medicine.
There are no adequate studies in women for determining infant risk when using this medication during breastfeeding. Weigh the potential benefits against the potential risks before taking this medication while breastfeeding. Although certain medicines should not be used together at all, in other cases two different medicines may be used together even if an interaction might occur.
In these cases, your doctor may want to change the dose, or other precautions may be necessary. When you are receiving this medicine, it is especially important that your healthcare professional know if you are taking any of the medicines listed below. The following interactions have been selected on the basis of their potential significance and are not necessarily all-inclusive. Using this medicine with any of the following medicines is usually not recommended, but may be required in some cases.
If both medicines are prescribed together, your doctor may change the dose or how often you use one or both of the medicines. Using this medicine with any of the following medicines may cause an increased risk of certain side effects, but using both drugs may be the best treatment for you. Certain medicines should not be used at or around the time of eating food or eating certain types of food since interactions may occur. Using alcohol or tobacco with certain medicines may also cause interactions to occur.
Discuss with your healthcare professional the use of your medicine with food, alcohol, or tobacco. The presence of other medical problems may affect the use of this medicine. Make sure you tell your doctor if you have any other medical problems, especially:.
A nurse or other trained health professional will give you this medicine in a hospital. This medicine is given through a needle placed in one of your veins. Your doctor will check your or your child's progress closely while you are receiving this medicine. This will allow your doctor to see if the medicine is working properly and to decide if you should continue to receive it.
Blood tests may be needed to check for unwanted effects. This medicine may cause a rare but serious type of an allergic reaction called an infusion reaction.
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