Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease.

We explored the fecal microbiota in pediatric patients <18 years of age with treatment-naïve IBD (80 Crohn's disease (CD), 27 ulcerative colitis (UC)), in 50 non-IBD patients with gastrointestinal symptoms without inflammation and in 75 healthy children. Using a targeted qPCR approach, the quantities of more than 100 different bacterial species were measured. Results: The bacterial abundance was statistically significantly reduced in the IBD and non-IBD patients compared to the healthy children for several beneficial species. The CD patients had a lower abundance of Bifidobacterium species compared to the UC patients, and the IBD patients in need of biologic therapy had a lower abundance of butyrate producing bacteria. Based on the abundance of bacterial species at diagnosis, we constructed Diagnostic, Phenotype and Prognostic Indexes. Patients with a high Diagnostic Index had 2.5 times higher odds for having IBD than those with a lower index. The CD patients had a higher Phenotype Index than the UC patients. Patients with a high Prognostic Index had 2.1 higher odds for needing biologic therapy compared to those with a lower index. Conclusions: The fecal abundance of bacterial species can aid in diagnosing IBD, in distinguishing CD from UC and in identifying children with IBD in need of biologic therapy.

Evolution and Population Dynamics of Clonal Complex 152 Community-Associated Methicillin-Resistant Staphylococcus aureus.

Since the late 1990s, changes in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) were recognized with the emergence of community-associated MRSA (CA-MRSA). CA-MRSA belonging to clonal complex 152 (CC152), carrying the small staphylococcal cassette chromosome mec (SCCmec) type V and encoding the Panton-Valentine leukocidin (PVL), has been observed in Europe. The aim of this study was to investigate its origin, evolution, and dissemination. Whole-genome sequencing was performed on a global collection of 149 CC152 isolates spanning 20 years (93 methicillin-susceptible S. aureus [MSSA] and 56 MRSA isolates). Core genome phylogeny, Bayesian inference, in silico resistance analyses, and genomic characterization were applied. Phylogenetic analysis revealed two major distinct clades, one dominated by MSSA and the other populated only by MRSA. The MSSA isolates were predominately from sub-Saharan Africa, whereas MRSA was almost exclusively from Europe. The European MRSA isolates all harbored an SCCmec type V (5C2&5) element, whereas other SCCmec elements were sporadically detected in MRSA from the otherwise MSSA-dominated clade, including SCCmec types IV (2B), V (5C2), and XIII (9A). In total, 93% of the studied CC152 isolates were PVL positive. Bayesian coalescent inference suggests an emergence of the European CC152-MRSA in the 1990s, while the CC152 lineage dates back to the 1970s. The CA-MRSA CC152 clone mimics the European CC80 CA-MRSA lineage by its emergence from a PVL-positive MSSA ancestor from North Africa or Europe. The CC152 lineage has acquired SCCmec several times, but acquisition of SCCmec type V (5C2&5) seems associated with expansion of MRSA CC152 in Europe.IMPORTANCE Understanding the evolution of CA-MRSA is important in light of the increasing importance of this reservoir in the dissemination of MRSA. Here, we highlight the story of the CA-MRSA CC152 lineage using whole-genome sequencing on an international collection of CC152. We show that the evolution of this lineage is novel and that antibiotic usage may have the potential to select for the phage-encoded Panton-Valentine leukocidin. The diversity of the strains correlated highly to geography, with higher level of resistance observed among the European MRSA isolates. The mobility of the SCCmec element is mandatory for the emergence of novel MRSA lineages, and we show here distinct acquisitions, one of which is linked to the successful clone found throughout Europe today.

Quantifying the transmission dynamics of MRSA in the community and healthcare settings in a low-prevalence country.

Methicillin-resistant Staphylococcus aureus (MRSA) is a primarily nosocomial pathogen that, in recent years, has increasingly spread to the general population. The rising prevalence of MRSA in the community implies more frequent introductions in healthcare settings that could jeopardize the effectiveness of infection-control procedures. To investigate the epidemiological dynamics of MRSA in a low-prevalence country, we developed an individual-based model (IBM) reproducing the population's sociodemography, explicitly representing households, hospitals, and nursing homes. The model was calibrated to surveillance data from the Norwegian national registry (2008-2015) and to published household prevalence data. We estimated an effective reproductive number of 0.68 (95% CI 0.47-0.90), suggesting that the observed rise in MRSA infections is not due to an ongoing epidemic but driven by more frequent acquisitions abroad. As a result of MRSA importations, an almost twofold increase in the prevalence of carriage was estimated over the study period, in 2015 reaching a value of 0.37% (0.25-0.54%) in the community and 1.11% (0.79-1.59%) in hospitalized patients. Household transmission accounted for half of new MRSA acquisitions, indicating this setting as a potential target for preventive strategies. However, nosocomial acquisition was still the primary source of symptomatic disease, which reinforces the importance of hospital-based transmission control. Although our results indicate little reason for concern about MRSA transmission in low-prevalence settings in the immediate future, the increases in importation and global circulation highlight the need for coordinated initiatives to reduce the spread of antibiotic resistance worldwide.

Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors.

Colorectal epithelial tumors occur spontaneously in dogs, and the pathogenesis seems to parallel that of humans. The development of human colorectal tumorigenesis has been linked to alterations in the composition of the intestinal microbiota. This study characterized the fecal- and mucosa-associated microbiota in dogs with colorectal epithelial tumors (n = 10). The fecal microbiota was characterized by 16S rDNA analysis and compared with that of control dogs (n = 13). We also determined the mucosa-associated microbiota composition in colonic tumor tissue (n = 8) and in adjacent non-tumor tissue (n = 5) by 16S rDNA- and rRNA profiling. The fecal microbial community structure in dogs with tumors was different from that of control samples and was distinguished by oligotypes affiliated with Enterobacteriaceae, Bacteroides, Helicobacter, Porphyromonas, Peptostreptococcus and Streptococcus, and lower abundance of Ruminococcaceae, Slackia, Clostridium XI and Faecalibacterium. The overall community structure and populations of mucosal bacteria were not different based on either the 16S rDNA or the 16S rRNA profile in tumor tissue vs. adjacent non-tumor tissue. However, the proportion of live, potentially active bacteria appeared to be higher in non-tumor tissue compared with tumor tissue and included Slackia, Roseburia, unclass. Ruminococcaeceae, unclass. Lachnospiraceae and Oscillibacter. Colorectal tumors are rarely diagnosed in dogs, but despite this limitation, we were able to show that dogs with colorectal tumors have distinct fecal microbiota profiles. These initial results support the need for future case-control studies that are adequately powered, as well as age-matched and breed-matched, in order to evaluate the influence of bacteria on colorectal cancer etiopathogenesis and to determine whether the bacteria may have potential as biomarkers in clinical settings.

Nasal carriage of Staphylococcus aureus: frequency and molecular diversity in a randomly sampled Norwegian community population.

A randomly selected, healthy Norwegian community population was studied for nasal carriage of Staphylococcus aureus (S. aureus) to describe frequency and molecular diversity in a non-hospital cohort (n = 95). Multilocus sequence typing revealed 31 sequence types (STs) belonging to 15 clonal complexes (CCs). The majority of isolates (71%) were classified as CC 15, 30 or 45. This clustering was confirmed by spa typing. There was no statistically significant difference in the distribution of CCs between this community population and a previously studied group of orthopaedic health care workers from a hospital in the same community. The study may indicate that microbial and host factors may be stronger determinants for S. aureus colonization than exposures associated with the hospital environment.

Distribution of methicillin-resistant Staphylococcus aureus in a low-prevalence area.

Investigating circulating methicillin-resistant Staphylococcus aureus (MRSA) strains and identifying their accumulations in society are important in the search for strategies for eradicating the pathogen. The aim of this study was to describe the distribution of MRSA in a low-prevalence area where MRSA could be establishing endemicity. MRSA isolates from 802 patients (803 isolates) were included and placed into a timeline (1991-2006) under different categories: hospital (n=270), long-term care facility (LTCF) (n=175) and general practitioner (GP) (n=358). MRSA isolates had been characterized using multilocus sequence-typing, staphylococcal cassette chromosome mec-typing and detection of Panton-Valentine leukocidin-encoding genes (lukS/F-PVL), and were placed in exotoxin-encoding gene clusters. The GP category increased mainly in a cluster with few exotoxin-encoding genes (r=0.760), the LTCF (r=0.804) and the hospital category (r=0.876) mainly in clusters with more exotoxin-encoding genes. ST8-IV, lukS/F-PVL present, increased in the community (1-41 isolates) in the time period 2002-2006, later in the hospital (1-8 isolates, 2004-2006), and finally reached the LTCF (1 isolate, 2006). ST8-IV, lukS/F-PVL absent, could have attained endemicity in LTCFs, where 51 isolates were isolated in 2006. ST125-IV, lukS/F-PVL absent, showing epidemic qualities abroad, caused outbreaks at five LTCFs.

Nasal carriage of Staphylococcus aureus: which sequence types do orthopedic surgical healthcare workers carry?

Using sequence typing methods, we found that healthcare workers on our orthopedic surgery unit were persistent carriers of a limited number of sequence types of Staphylococcus aureus for a limited time. Multilocus sequence typing characterized 3 clonal complexes that accounted for more than 80% of the clonal complexes identified.