Interplay between gut microbiota and antibiotics

The human body is colonized by a vast number of microorganisms collectively defined as the microbiota. In the gut, the microbiota has important roles in health and disease, and can serve as a host of antibiotic resistance genes. Disturbances in the ecological balance, e.g. by antibiotics, can affect the diversity and dynamics of the microbiota. The extent of the disturbance induced by antibiotics is influenced by, among other factors, the class of antibiotic, the dose, and administration route. One of the most common consequences of excessive antibiotic use is the emergence of antibiotic resistant bacteria and the dissemination of the corresponding resistance genes to other microbial inhabitants of the gut community, in addition to affecting the colonization resistance and promoting the overgrowth of pathogens. These effects are particularly relevant for Intensive Care Unit (ICU) patients, which are frequently exposed to a high risk of hospital-acquired infections associated with antibiotic resistant bacteria. Due to the important roles that members of the gut microbiota play in the host, including their role as potential hubs for the dissemination of antibiotic resistance, recent research has focused on determining the composition and function of gut microorganisms and the antibiotic resistance genes associated with them. The objectives of the research described in this thesis were to study the diversity and dynamics of the gut microbiota and resistome in ICU patients receiving antibiotic prophylactic therapy, and to assess the colonization dynamics with antibiotic resistant bacteria focusing on the commensal microbiota as a reservoir of antibiotic resistance genes by using culture dependent and independent techniques. Furthermore, the genetic background involved in the subsistence phenotype was investigated to disentangle the links between resistance and subsistence. Bacteria harbor antibiotic resistance genes that participate in a range of processes such as resisting the toxic effects of antibiotics, but could also aid in the utilization of antibiotics as sole carbon source, referred to as antibiotic subsistence phenotype. In chapter 2, the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics was investigated. Various gut isolates of Escherichia coli and Cellulosimicrobium spp. displayed the subsistence phenotype, mainly with aminoglycosides. Although no antibiotic degradation could be detected, the number of colony forming units increased during growth in medium with only the antibiotic as a carbon source. By using different approaches to study the aminoglycoside subsistence phenotype, we observed that laboratory strains carrying the aminoglycoside 3’phosphotransferase II gene also displayed the subsistence phenotype on aminoglycosides and that glycosyl-hydrolases seem to be involved in the subsistence phenotype. As the zoo animals for which the subsistence phenotype was investigated also included a number of non-human primates, the applicability of Human Intestinal Tract Chip (HITChip) to study the gut microbiota composition of these animals was assessed, including a comparison with healthy human volunteers (Chapter 3). It was concluded that the HITChip can be successfully applied to the gut microbiota of closely related hominids, and the microbiota dynamics can therefore be quickly assessed by the HITChip. In Chapter 4, a combination of 16S rRNA phylogenetic profiling using the HITChip and metagenomics sequencing was implemented on samples from a single ICU hospitalized patient that received antibiotic prophylactic therapy (Selective Digestive Decontamination - SDD). The different approaches showed a highly dynamic microbiota composition over time and the prevalence of aminoglycoside resistance genes harbored by a member of the commensal anaerobic microbiota, highlighting the role of the commensal microbiota as a reservoir of antibiotic resistance genes. As an extension of this study (Chapter 5), 11 ICU patients receiving SDD were followed using 10 healthy individuals as a control group to compare the diversity and dynamics of the gut microbiota and resistome by HITChip and nanolitre-scale quantitative PCRs, respectively. The microbial diversity of the healthy individuals was higher compared to ICU patients, and it was less dynamic compared to ICU patients under antibiotic treatment. Likewise, the levels of antibiotic resistance genes increased in ICU patients compared to healthy individuals, indicating that during ICU hospitalization and the SDD, gut microbiota diversity and dynamics are profoundly affected, including the selection of antibiotic resistance in anaerobic commensal bacteria. This was further expanded in an extensive study focusing on colonization dynamics with antibiotic resistant bacteria as described in Chapter 6. This was performed in the same group of ICU-hospitalized patients receiving SDD therapy and showed that by using a range of culture media and selective conditions a variety of taxonomic groups could be isolated, including aerobic and anaerobic antibiotic resistant bacteria. The overall composition of the faecal microbiota detected by HITChip indicated mainly a decrease of Enterobacteriaceae and an increase of the enterococcal population. Since critically ill patients are susceptible to hospital-acquired infections and the control of the emergence of antibiotic resistance is crucial to improve therapeutic outcomes, an extended analysis of the Enterococcus colonization dynamics in this group of patients by cultivation and phenotypic and genotypic characterization of the isolates provided new information about carriage of antibiotic resistance and virulence factor encoding genes (Chapter 7). It also highlighted the opportunity for the exchange of resistance and virulence genes, which could increase the risk of acquiring nosocomial infections. Next, chapter 8 described the implementation of high-throughput cultivation-based screening using the Microdish platform combined with high-throughput sequencing (MiSeq) using faecal samples from ICU patients receiving SDD. This allowed for the recovery of previously uncultivable bacteria, including a pure culture of a close relative of Sellimonas intestinalis BR72T that was isolated from media containing tobramycin, cefotaxime and polymyxin E. This strain could therefore represent a potential antibiotic resistance reservoir. In conclusion, this thesis provides broad insight into the diversity and dynamics of the gut microbiota and resistome in ICU hospitalized patients receiving SDD therapy as well as the dynamics of colonization with antibiotic resistant bacteria. Especially our extensive study of the colonization dynamics of Enterococcus spp. during ICU stay reinforced the notion that SDD therapy does not cover this group of bacteria and highlights the importance of a critical control of the emergence of antibiotic resistance in enterococci and their spread and dissemination as known potential pathogens. Furthermore, the extensive use of antibiotics could select for an increase in the rate of antibiotic resistance against aminoglycosides and beta-lactams, indicating that a control in the use of broad spectrum antibiotics needs to be considered. In addition, this thesis provides evidence regarding the possible genetic background involved in the subsistence phenotype, however, future studies on metabolic pathways could provide novel insight into the underlying mechanisms.