Enterobacteriaceae and Bacteroidaceae provide resistance to travel-associated intestinal colonization by multi-drug resistant Escherichia coli

Metagenomic changes in response to antibiotic treatment in severe orthopedic trauma patients

We investigated changes in microbiome composition and abundance of antimicrobial resistance (AMR) genes post-antibiotic treatment in severe trauma patients. Shotgun sequencing revealed beta diversity (Bray-Curtis) differences between 16 hospitalized multiple rib fractures patients and 10 age- and sex-matched controls (p = 0.043), and between antibiotic-treated and untreated patients (p = 0.015). Antibiotic-treated patients had lower alpha diversity (Shannon) at discharge (p = 0.003) and 12-week post-discharge (p = 0.007). At 12 weeks, they also exhibited a 5.50-fold (95% confidence interval [CI]: 2.86-8.15) increase in Escherichia coli (p = 0.0004) compared to controls. Differential analysis identified nine AMRs that increased in antibiotic-treated compared to untreated patients between hospital discharge and 6 and 12 weeks follow-up (false discovery rate [FDR] < 0.20). Two aminoglycoside genes and a beta-lactamase gene were directly related to antibiotics administered, while five were unrelated. In trauma patients, lower alpha diversity, higher abundance of pathobionts, and increases in AMRs persisted for 12 weeks post-discharge, suggesting prolonged microbiome disruption. Probiotic or symbiotic therapies may offer future treatment avenues.

Global Dynamics of Gastrointestinal Colonisations and Antimicrobial Resistance: Insights from International Travellers to Low- and Middle-Income Countries

Gastrointestinal microorganism resistance and dissemination are increasing, partly due to international travel. This study investigated gastrointestinal colonisations and the acquisition of antimicrobial resistance (AMR) genes among international travellers moving between Spain and low- and middle-income countries (Peru and Ethiopia). We analysed 102 stool samples from 51 volunteers collected before and after travel, revealing significantly higher rates of colonisation by both bacteria and protists upon return. Diarrhoeagenic strains of E. coli were the most notable microorganism detected using RT-PCR with the Seegene Allplex™ Gastrointestinal Panel Assays. A striking prevalence of β-lactamase resistance genes, particularly the TEM gene, was observed both before and after travel. No significant differences in AMR genes were found between the different locations. These findings highlight the need for rigorous surveillance and preventive strategies, as travel does not significantly impact AMR gene acquisition but does affect microbial colonisations. This study provides valuable insights into the intersection of gastrointestinal microorganism acquisition and AMR in international travellers, underscoring the need for targeted interventions and increased awareness.

The Roles of a Multidrug-Resistant Klebsiella pneumoniae High-Risk Clone and Its Resistance Plasmids on the Gastrointestinal Colonization and Host-Defense Effectors in the Gut

The asymptomatic gastrointestinal colonization of multidrug-resistant (MDR) bacteria can lead to difficult-to-treat infections. We investigated the role of host factors influencing colonization in an orogastrical murine infection model using a CTX-M-15- and OXA-162-producing Klebsiella pneumoniae ST15 (MDR-KP) strain, as well as Escherichia coli J53 (EC) and E. coli transconjugants with an IncFII(K) plasmid carrying CTX-M-15 (EC-CTXM), and with an IncL plasmid carrying OXA-162 (EC-OXA) genes. The fecal bacterial count in colony-forming unit/gram stool (CFU/g) was determined by cultivation, IgA and defensin levels by ELISA, and gut microbiota by 16S rRNA analysis. The CFU was the lowest in EC, followed by EC-OXA and EC-CTXM, and the highest in the MDR-KP group. The IgA level in feces increased in MDR-KP, EC-CTXM, and EC-OXA, and did not change in EC. The beta-defensin 3 level markedly increased in all groups, with the highest values in MDR-KP and EC-CTXM. Alpha-defensin-5 increased in all groups especially in EC. In microbiota, the Bacteroidota phylum was dominant in MDR-KP, EC-CTXM, and EC-OXA, whereas Proteobacteria was dominant in EC. The Muribaculaceae family was significantly more common in the MDR-KP and EC-OXA groups, while the Lachnospiraceae family was dominant in the EC group. While fecal IgA levels positively correlated with colonizing bacterial CFU, the alpha-defensin 5 levels inversely correlated with CFUs and IgA levels. The presence of the IncFII(K) plasmid induced beta-defensin 3 production. The amounts of the Muribaculaceae family members exhibited a correlation with the IncL plasmid. The detected amounts of the Lachnospiraceae family indicated the protective role against the high-risk clone and the resistance plasmids' dissemination. Our results suggest that not only the MDR-KP clone itself but also the resistance plasmids play a primary role in the colonization rate in the gastrointestinal tract. Both the MDR-KP clone as well as the IncFII(K) and IncL resistance plasmids provide survival and colonization benefits in the gut.

Gut microbiome dynamics in index patients colonized with extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales after hospital discharge and their household contacts

IMPORTANCE

Colonization with extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) often precedes infections and is therefore considered as a great threat for public health. Here, we studied the gut microbiome dynamics in eight index patients colonized with ESBL-PE after hospital discharge and the impact of exposure to this index patient on the gut microbiome dynamics of their household contacts. We showed that the microbiome composition from index patients is different from their household contacts upon hospital discharge and that, in some of the index patients, their microbiome composition over time shifted toward the composition of their household contacts. In contrast, household contacts showed a stable microbiome composition over time irrespective of low-level extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) or extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) gut colonization, suggesting that, in healthy microbiomes, colonization resistance is able to prevent ESBL-PE expansion.

Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages

The repeated emergence of multi-drug-resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug-resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. Given the rapid colonization observed in travel studies, it is possible that the presence of a type VI secretion system (T6SS) may be responsible for the rapid competitive advantage of drug-resistant E. coli clones. We employed large-scale genomic approaches to investigate this hypothesis. First, we searched for T6SS genes across a curated dataset of over 20 000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene carriage and MDR lineages. However, multiple clades containing MDR clones have lost essential structural T6SS genes. We characterized the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones.

Multidrug-resistant E. coli encoding high genetic diversity in carbohydrate metabolism genes displace commensal E. coli from the intestinal tract

Extra-intestinal pathogenic Escherichia coli (ExPEC) can cause a variety of infections outside of the intestine and are a major causative agent of urinary tract infections. Treatment of these infections is increasingly frustrated by antimicrobial resistance (AMR) diminishing the number of effective therapies available to clinicians. Incidence of multidrug resistance (MDR) is not uniform across the phylogenetic spectrum of E. coli. Instead, AMR is concentrated in select lineages, such as ST131, which are MDR pandemic clones that have spread AMR globally. Using a gnotobiotic mouse model, we demonstrate that an MDR E. coli ST131 is capable of out-competing and displacing non-MDR E. coli from the gut in vivo. This is achieved in the absence of antibiotic treatment mediating a selective advantage. In mice colonised with non-MDR E. coli strains, challenge with MDR E. coli either by oral gavage or co-housing with MDR E. coli colonised mice results in displacement and dominant intestinal colonisation by MDR E. coli ST131. To investigate the genetic basis of this superior gut colonisation ability by MDR E. coli, we assayed the metabolic capabilities of our strains using a Biolog phenotypic microarray revealing altered carbon metabolism. Functional pangenomic analysis of 19,571 E. coli genomes revealed that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. The data presented here demonstrate that independent of antibiotic selective pressures, MDR E. coli display a competitive advantage to colonise the mammalian gut and points to a vital role of metabolism in the evolution and success of MDR lineages of E. coli via carriage and spread.

Resistome expansion in disease-associated human gut microbiomes

BACKGROUND

The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome.

RESULTS

The human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer.

CONCLUSIONS

Diseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.

Gut Microbiota Dysbiosis and Increased NLRP3 Levels in Patients with Pregnancy-Induced Hypertension

Pregnancy-induced hypertension (PIH) is one of the most common diseases, causing high maternal morbidity and mortality. However, the correlation of gut microbiota in PIH has not been reported. Our aim was to characterize the intestinal microbiota of patients with PIH compared with healthy people. We analyzed and compared the gut microbiota communities in the feces of 28 PIH patients with pregnancy(not pre-pregnancy) body mass index (including height and weight)-matched healthy controls using 16S rRNA gene sequencing and then investigate the relationships among gut microbiota, cytokines, and PIH. Compared with the healthy group, microbial α diversity was lower in the PIH group, but not statistically significant different. At the phylum level, Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria exhibited obvious differences between the PIH and control groups. LEfSe analysis found 33 differentially abundant taxa between the two groups. The production of pro-inflammatory cytokines in PIH serum or placenta tissues was higher than that of the control group. In addition to alterations in gut microbiota composition, we also found that the Bac_Prevotellaceae, Pre_Prevotella bacteria were positively correlated with NLRP3 level, but negatively correlated with Bac_Bacteroidaceae, Bac_Bacteroides. PIH patients had gut microbiota dysbiosis and increased NLRP3 levels, which will lead to a better understanding of the relationship between the gut microbiota and PIH.

Shorter sleep time relates to lower human defensin 5 secretion and compositional disturbance of the intestinal microbiota accompanied by decreased short-chain fatty acid production

Sleep is essential for our health. Short sleep is known to increase disease risks via imbalance of intestinal microbiota, dysbiosis. However, mechanisms by which short sleep induces dysbiosis remain unknown. Small intestinal Paneth cell regulates the intestinal microbiota by secreting antimicrobial peptides including α-defensin, human defensin 5 (HD5). Disruption of circadian rhythm mediating sleep-wake cycle induces Paneth cell failure. We aim to clarify effects of short sleep on HD5 secretion and the intestinal microbiota. Fecal samples and self-reported sleep time were obtained from 35 healthy middle-aged Japanese (41 to 60-year-old). Shorter sleep time was associated with lower fecal HD5 concentration (r = 0.354, p = 0.037), lower centered log ratio (CLR)-transformed abundance of short-chain fatty acid (SCFA) producers in the intestinal microbiota such as [Ruminococcus] gnavus group (r = 0.504, p = 0.002) and Butyricicoccus (r = 0.484, p = 0.003), and lower fecal SCFA concentration. Furthermore, fecal HD5 positively correlated with the abundance of these genera and SCFA concentration. These findings suggest that short sleep relates to disturbance of the intestinal microbiota via decreased HD5 secretion.