Emergence of Raoultella ornithinolytica in human infections from different hospitals in Ecuador with OXA-48-producing resistance.

Purpose: The purpose of this study was to highlight the clinical and molecular features of 13 Raoultella ornithinolytica strains isolated from clinical environments in Ecuador, and to perform comparative genomics with previously published genomes of Raoultella spp. As Raoultella is primarily found in environmental, clinical settings, we focused our work on identifying mechanisms of resistance that can provide this bacterium an advantage to establish and persist in hospital environments. Methods: We analyzed 13 strains of Raoultella ornithinolytica isolated from patients with healthcare associated infections (HAI) in three hospitals in Quito and one in Santo Domingo de Los Tsáchilas, Ecuador, between November 2017 and April 2018. These isolates were subjected to phenotypic antimicrobial susceptibility testing, end-point polymerase chain reaction (PCR) to detect the presence of carbapenemases and whole-genome sequencing. Results: Polymerase chain reaction revealed that seven isolates were positive isolates for blaOXA-48 and one for blaKPC-2 gene. Of the seven strains that presented the blaOXA-48 gene, six harbored it on an IncFII plasmid, one was inserted into the bacterial chromosome. The blaKPC gene was detected in an IncM2/IncR plasmid. From the bioinformatics analysis, nine genomes had the gene blaOXA-48, originating from Ecuador. Moreover, all R. ornithinolytica strains contained the ORN-1 gene, which confers resistance for ß-lactams, such as penicillins and cephalosporins. Comparative genome analysis of the strains showed that the pangenome of R. ornithinolytica is considered an open pangenome, with 27.77% of core genes, which could be explained by the fact that the antibiotic resistance genes in the ancestral reconstruction are relatively new, suggesting that this genome is constantly incorporating new genes. Conclusion: These results reveal the genome plasticity of R. ornithinolytica, particularly in acquiring antibiotic-resistance genes. The genomic surveillance and infectious control of these uncommon species are important since they may contribute to the burden of antimicrobial resistance and human health.

Exploring the similarities and differences amongst service users with and without learning disabilities attending Saint Marys Sexual Assault Referral Centre.

BACKGROUND: People with learning disabilities are over-represented amongst Sexual Assault Referral Centre service users. This work aims to explore the similarities and differences between service users with and without learning disabilities. METHOD: Medical notes of 52 service users likely to have a learning disability were compared with 52 service users not likely to have a learning disability (according to the Learning Disability Screening Questionnaire); all of whom attended Saint Marys SARC for a forensic medical examination during a 12-month period. RESULTS: Significant associations were found between the likelihood of learning disability and relationship to perpetrator; location of assault; alcohol use; time taken to present to SARC; domestic violence; self-harm; suicide attempts and mental health service involvement. CONCLUSIONS: People with learning disabilities in the sexually assaulted population are more likely to present with intersecting vulnerabilities emphasising the need for timely, accessible and appropriate patient-centred care for this group.

Evidence of natural selection and dominance of SARS-CoV-2 variant Lambda (C.37) over variants of concern in Cusco, Peru.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage C.37 (Lambda) has spread rapidly in Peru and other Latin American countries. However, most studies in Peru have focused on Lima, the capital city, without knowing the dynamics of the spread of the variant in other departments. Cusco, Peru, is one of the most popular departments in the country for tourists, so the introduction of new variants of SARS-CoV-2 might occur despite closure of the borders. Therefore, in this work, we analyzed the variants circulating in Cusco. The aim of this work was to better understand the distribution of SARS-CoV-2 lineages circulating in Cusco and to characterize the genomes of these strains. To this end, 46 SARS-CoV-2 genomes from vaccinated and unvaccinated patients were sequenced in the first half of 2021. The genomes were analyzed using phylogenetic and natural selection methods. Phylogenetic trees from Cusco showed dominance of the Lambda lineage over the variants of concern (VOCs), and there was no clustering of variants by district. Natural selection analysis revealed mutations, mainly in the spike protein, at positions 75, 246, 247, 707, 769, and 1020. In addition, we found that unvaccinated patients accumulated more new mutations than did vaccinated patients, and these included the F101Y mutation in ORF7a, E419A in NSP3, a deletion in S (21,618-22,501), and a deletion in ORF3a (25,437-26,122).

The Microbial Composition in Circumneutral Thermal Springs from Chignahuapan, Puebla, Mexico Reveals the Presence of Particular Sulfur-Oxidizing Bacterial and Viral Communities.

Terrestrial thermal springs are widely distributed globally, and these springs harbor a broad diversity of organisms of biotechnological interest. In Mexico, few studies exploring this kind of environment have been described. In this work, we explore the microbial community in Chignahuapan hot springs, which provides clues to understand these ecosystems' diversity. We assessed the diversity of the microorganism communities in a hot spring environment with a metagenomic shotgun approach. Besides identifying similarities and differences with other ecosystems, we achieved a systematic comparison against 11 metagenomic samples from diverse localities. The Chignahuapan hot springs show a particular prevalence of sulfur-oxidizing bacteria from the genera Rhodococcus, Thermomonas, Thiomonas, Acinetobacter, Sulfurovum, and Bacillus, highlighting those that are different from other recovered bacterial populations in circumneutral hot springs environments around the world. The co-occurrence analysis of the bacteria and viruses in these environments revealed that within the Rhodococcus, Thiomonas, Thermonas, and Bacillus genera, the Chignahuapan samples have specific species of bacteria with a particular abundance, such as Rhodococcus erytropholis. The viruses in the circumneutral hot springs present bacteriophages within the order Caudovirales (Siphoviridae, Myoviridae, and Podoviridae), but the family of Herelleviridae was the most abundant in Chignahuapan samples. Furthermore, viral auxiliary metabolic genes were identified, many of which contribute mainly to the metabolism of cofactors and vitamins as well as carbohydrate metabolism. Nevertheless, the viruses and bacteria present in the circumneutral environments contribute to the sulfur cycle. This work represents an exhaustive characterization of a community structure in samples collected from hot springs in Mexico and opens opportunities to identify organisms of biotechnological interest.

The disproportionately high prevalence of learning disabilities amongst adults attending Saint Marys Sexual Assault Referral Centre.

BACKGROUND: There is a dearth of reliable data on sexual assault prevalence amongst people with learning disabilities. This work aims to identify the prevalence of learning disabilities amongst adult clients attending Saint Marys Sexual Assault Referral Centre and ascertain the similarities/differences amongst clients with learning disabilities as compared to clients without. METHOD: A short validated Learning Disability Screening Questionnaire was completed by adult clients attending Saint Marys for a forensic medical examination during a twelve-month period. RESULTS: Amongst 679 clients who attended for an FME and completed the LDSQ, 8.2% were likely to have a learning disability and the presence of self-reported: mental health issues (X2  = 11.24, p = .001), self-harm (X2  = 5.63, p = .017) and substance misuse (X2  = 13.15906, p = .001). CONCLUSIONS: Consistent with the broader literature, people with learning disability were over-represented in the sexually assaulted population emphasizing the importance of timely, accessible and appropriate patient-centred care for this vulnerable group.

Comment on "Nodal infection in Markovian susceptible-infected-susceptible and susceptible-infected-removed epidemics on networks are non-negatively correlated".

Cator and Van Mieghem [Phys. Rev. E 89, 052802 (2014)PLEEE81539-375510.1103/PhysRevE.89.052802] stated that the correlation of infection at the same time between any pair of nodes in a network is non-negative for the Markovian susceptible-infected-susceptible (SIS) and susceptible-infected-removed (SIR) epidemic models. The arguments used to obtain this result rely strongly on the graphical construction of the stochastic process, as well as the Fortuin, Kasteleyn, and Ginibre (FKG) inequality. In this Comment, we show that although the approach used by the authors applies to the SIS model, it cannot be used for the SIR model as stated in their work. In particular, we observe that monotonicity in the process is crucial for invoking the FKG inequality. Moreover, we provide an example of a simple graph for which the nodal infection in the SIR Markovian model is negatively correlated.