Background Escherichia coli lineage ST131 predominates across various spectra of extra-intestinal infections, including urinary tract infection (UTI). The distinctive resistance profile, diverse armamentarium of virulence factors and rapid global dissemination of ST131 E. coli makes it an intriguing pathogen. However, not much is known about the prevalence and genetic attributes of ST131 lineage in Pakistan. Methods We estimated prevalence and genetic attributes of E. coli ST131 isolates causing UTI among 155 randomly selected samples. Samples were analyzed for phylogenetic grouping, O-typing and fum C/ fim H typing. Isolates were further tested for the ESBL and virulence factors using PCR. Results Overall, 59% of the UPEC isolates belonged to the phylogenetic group B2, followed by D = 28%, B1 = 8% and A = 5%. Among 18 different Sequence-types, ST131 was the dominant lineage ( n = 71; 46%) out of which 72% of the isolates were assigned to the phylogenetic group B2, while 61% adhered to the serogroup O25b. Fum C/ fim H typing confirmed 49% of the ST131 as H30 sub-types. In this study, significant numbers of the identified ST131 isolates were MDR and 42% showed ESBL phenotypes, out of which 37% carried bla - CTX-M-15 . Moreover, different virulence factors were detected in following percentages: fim H,155(100%), iut A 86 (55%), feo B 76 (49%), pap C 75 (48%), papGII 70 (45%), kpsMTII 40 (26%), pap EF 37 (24%), fyu A 37 (24%), usp 22 (14%), pap A 20 (13%), sfa/foc 20 (13%), hly A 18 (12%), afa 15 (10%), cdt B 11 (7%), papGI 6 (4%), papGIII 6 (4%), kpsMTIII 4 (3%) and bma E2 (1%). Conclusion Conclusively, this study provides important insight into the genetic and virulence attributes of pandemic MDR ST131 strains involved in UTIs. It also highlights higher prevalence of ST131-O25b-H30 UPEC isolates in patients, which was previously unreported from this part of globe.

These data indicate that oral intake of ABA-PEG20k-Pi20 may be an effective agent to contain the virulence of E. faecalis and may prevent anastomotic leak caused by this organism. Clinical relevance Progress in understanding the pathogenesis of anastomotic leak continues to point to intestinal bacteria as key causative agents. The presence of pathogens such as Enterococcus faecalis that predominate on anastomotic tissues despite antibiotic use, coupled with their ability to produce collagenase, appears to alter the process of healing that leads to leakage. Further antibiotic administration may seem logical, but carries the unwanted risk of eliminating the normal microbiome, which functions competitively to exclude and suppress the virulence of pathogens such as E. faecalis. Therefore, non-antibiotic strategies that can suppress the production of collagenase by E. faecalis without affecting its growth, or potentially normal beneficial microbiota, may have unique advantages. The findings of this study demonstrate that drinking a phosphate-based polymer can achieve the goal of preventing anastomotic leak by suppressing collagenase production in E. faecalis without affecting its growth.

Background Early childhood caries (ECC)—dental caries (cavities) occurring in primary teeth up to age 6 years—is a prevalent childhood oral disease with a microbial etiology. Streptococcus mutans was previously considered a primary cause, but recent research promotes the ecologic hypothesis, in which a dysbiosis in the oral microbial community leads to caries. In this incident, density sampled case-control study of 189 children followed from 2 months to 5 years, we use the salivary bacteriome to (1) prospectively test the ecological hypothesis of ECC in salivary bacteriome communities and (2) identify co-occurring salivary bacterial communities predicting future ECC. Results Supervised classification of future ECC case status using salivary samples from age 12 months using bacteriome-wide data (AUC-ROC 0.78 95% CI (0.71–0.85)) predicts future ECC status before S. mutans can be detected. Dirichlet multinomial community state typing and co-occurrence network analysis identified similar robust and replicable groups of co-occurring taxa. Mean relative abundance of a Haemophilus parainfluenzae/Neisseria/Fusobacterium periodonticum group was lower in future ECC cases (0.14) than controls (0.23, P value < 0.001) in pre-incident visits, positively correlated with saliva pH (Pearson rho = 0.33, P value < 0.001) and reduced in individuals who had acquired S. mutans by the next study visit (0.13) versus those who did not (0.20, P value < 0.01). In a subset of whole genome shotgun sequenced samples (n = 30), case plaque had higher abundances of antibiotic production and resistance gene orthologs, including a major facilitator superfamily multidrug resistance transporter (MFS DHA2 family PBH value = 1.9 × 10−28), lantibiotic transport system permease protein (PBH value = 6.0 × 10−6) and bacitracin synthase I (PBH value = 5.6 × 10−6). The oxidative phosphorylation KEGG pathway was enriched in case plaque (PBH value = 1.2 × 10−8), while the ABC transporter pathway was depleted (PBH value = 3.6 × 10−3). Conclusions Early-life bacterial interactions predisposed children to ECC, supporting a time-dependent interpretation of the ecological hypothesis. Bacterial communities which assemble before 12 months of age can promote or inhibit an ecological succession to S. mutans dominance and cariogenesis. Intragenera competitions and intergenera cooperation between oral taxa may shape the emergence of these communities, providing points for preventive interventions.

Background Vancomycin-resistant Enterococcus faecium and Enterococcus faecalis frequently colonize nursing facility (NF) residents, creating opportunities for vancomycin-resistant Enterococcus (VRE) transmission and dissemination of mobile genetic elements conferring antimicrobial resistance. Most VRE studies do not speciate; our study addresses this lack and compares the epidemiology of E faecium and E faecalis. Methods We enrolled 651 newly admitted patients from 6 different NFs and collected swabs from several body sites at enrollment, 14 days, 30 days, and monthly thereafter for up to 6 months. The VRE were speciated using a duplex polymerase chain reaction. We used multinomial logistic regression models to compare risk factors associated with colonization of E faecium and E faecalis. Results Overall, 40.7% were colonized with E faecium, E faecalis, or both. At enrollment, more participants were colonized with E faecium (17.8%) than E faecalis (8.4%); 3.2% carried both species. Enterococcus faecium was carried twice as long as E faecalis (69 days and 32 days, respectively), but incidence rates were similar (E faecium, 3.9/1000 person-days vs E faecalis, 4.1/1000 person-days). Length of stay did not differ by species among incident cases. Residents who used antibiotics within the past 30 days had a greater incidence of both E faecium (odds ratio [OR] = 2.89; 95% confidence interval [CI], 1.82–4.60) and E faecalis (OR = 1.80; 95% CI, 1.16–2.80); device use was most strongly associated with the incidence of E faecium colonization (OR = 2.01; 95% CI, 1.15–3.50). Conclusions Recent increases in vancomycin-resistant E faecium prevalence may reflect increased device use and longer duration of carriage.

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