Carbapenem-resistant Enterobacteriaceae (CRE) is a risk to public health worldwide and causes epidemic outbreaks in hospitals. The identification of alterations in the gut microbial profile can potentially serve as an early diagnostic tool to prevent harmful bacterial colonization. The purpose of this study was to characterize the gut microbiota profile of CRE-positive stool samples using 16S rRNA gene sequencing and to compare it with that of healthy control groups at King AbdulAziz University Hospital. Our results demonstrate that compared to the control group samples, the CRE-positive and CRE-negative group samples were less diverse and were dominated by a few operational taxonomic clusters of Enterococcus, Sphingomonas, and Staphylococcus. An analysis of samples from CRE-positive patients revealed Pseudomonas as the most abundant taxon. The existence of Pseudomonas in clinical samples undoubtedly indicates the development of resistance to a variety of antimicrobial drugs, with a less diverse microbiota. In our study, we found that the co-occurrence patterns of Klebsiella, Parabacteroides, Proteus and Pseudomonas differed between the CRE-negative and control stool groups.

Carbapenem-resistant Enterobacteriaceae (CRE) is a risk to public health worldwide and causes epidemic outbreaks in hospitals. The identification of alterations in the gut microbial profile can potentially serve as an early diagnostic tool to prevent harmful bacterial colonization. The purpose of this study was to characterize the gut microbiota profile of CRE-positive stool samples using 16S rRNA gene sequencing and to compare it with that of healthy control groups at King AbdulAziz University Hospital. Our results demonstrate that compared to the control group samples, the CRE-positive and CRE-negative group samples were less diverse and were dominated by a few operational taxonomic clusters of Enterococcus, Sphingomonas, and Staphylococcus. An analysis of samples from CRE-positive patients revealed Pseudomonas as the most abundant taxon. The existence of Pseudomonas in clinical samples undoubtedly indicates the development of resistance to a variety of antimicrobial drugs, with a less diverse microbiota. In our study, we found that the co-occurrence patterns of Klebsiella, Parabacteroides, Proteus and Pseudomonas differed between the CRE-negative and control stool groups.

In this study, we present for the first time the landscape of the lung microbiota in patients with ventilator-associated pneumonia in Intensive Care Units in Saudi Arabia. DNA from 83 deep endotracheal aspirate lung samples was subjected to PacBio sequencing to identify pathogens in comparison with conventional diagnostic techniques. Patients on ventilation with pneumonia presented with similar lung flora to those of patients on ventilation without pneumonia. Proteobacteria, Firmicutes, and Bacteroidetes were detected in the majority of the samples. Samples treated with different antibiotics exhibited similar abundances of phyla and families. In order, the ten most common species detected in 16 clusters were Klebsiella pneumoniae, Stenotrophomonas maltophilia, Haemophilus influenzae, Pseudomonas aeruginosa, Metamycoplasma salivarium, Elizabethkingia anophilis, Staphylococcus aureus, Acinetobacter baumannii, Prevotella oris and Klebsiella africana. Of 51 on ventilation with pneumonia, the pathogens identified through sequencing corresponded with the findings from culture-dependent tests in 26 patients (50.98%), whereas the results differed in 30 patients (58.82%). Of 32 patients on ventilation without pneumonia, the pathogens identified through sequencing matched the conventional diagnostics results in only two patients (6.25%) but differed in 25 patients (78.13%). In summary, patients on mechanical ventilation with pneumonia did not display notable phenotypic traits. K. pneumoniae and S. maltophilia were the most common taxa detected in the samples, although some variations in microbial composition were observed. We conclude that Intensive Care Units exhibit distinct patterns of microbial colonization.

Flavobacterium suncheonense is a member of the family Flavobacteriaceae in the phylum Bacteroidetes. Strain GH29-5^T (DSM 17707^T) was isolated from greenhouse soil in Suncheon, South Korea. F. suncheonense GH29-5^T is part of the GenomicEncyclopedia ofBacteria andArchaea project. The 2,880,663 bp long draft genome consists of 54 scaffolds with 2739 protein-coding genes and 82 RNA genes. The genome of strain GH29-5^T has 117 genes encoding peptidases but a small number of genes encoding carbohydrate active enzymes (51 CAZymes). Metallo and serine peptidases were found most frequently. Among CAZymes, eight glycoside hydrolase families, nine glycosyl transferase families, two carbohydrate binding module families and four carbohydrate esterase families were identified. Suprisingly, polysaccharides utilization loci (PULs) were not found in strain GH29-5^T. Based on the coherent physiological and genomic characteristics we suggest that F. suncheonense GH29-5^T feeds rather on proteins than saccharides and lipids.