Characterisation and risk factor profiling of Pseudomonas aeruginosa urinary tract infections: pinpointing those likely to be caused by multidrug-resistant strains

This study aimed to characterise UTIs caused by Pseudomonas aeruginosa in hospitalised adults and to identify risk factors for infections caused by multidrug-resistant (MDR) strains. A retrospective case–case–control study was conducted in two Italian teaching hospitals. Totally, 242 monomicrobial P. aeruginosa UTIs were analysed; 65 (26.9%) were caused by MDR strains. Clinical treatment failure at 72 h in 215 patients receiving empirical therapy was more frequent in MDR versus non-MDR cases [35/59 (59.3%) vs. 55/156 (35.3%); P = 0.001], particularly when a β-lactam/β-lactamase inhibitor or fluoroquinolone was initially prescribed. By Day 7 (when all regimens were consistent with antimicrobial susceptibility results), treatment failure rates were similar [MDR 15/65 (23.1%) vs. non-MDR 25/177 (14.1%); P = 0.09]. In-hospital mortality rates remained low in both groups [6/65 (9.2%) vs. 22/177 (12.4%); P = 0.49], but median hospital stay for MDR cases was longer (48 vs. 22 days; P ≤ 0.001). Models for predicting MDR and non-MDR P. aeruginosa UTIs displayed good discriminatory power. Presence of ≥3 risk factors for MDR P. aeruginosa UTI was associated with an OR for this outcome of 7.44 (95% CI 3.24–17.57; P < 0.001; specificity 91%, accuracy 75%). The model for predicting non-MDR P. aeruginosa UTI displayed similar accuracy (74%) with a risk factor burden threshold of ≥2 (OR = 7.02, 95% CI 4.61–10.70; P < 0.001). Risk factor assessment can identify UTIs in hospitalised patients likely to be caused by MDR P. aeruginosa, thereby facilitating targeted infection control and timelier effective treatment.     

Eurasiaplex: A forensic SNP assay for differentiating European and South Asian ancestries

We have selected a set of single nucleotide polymorphisms (SNPs) with the specific aim of differentiating European and South Asian ancestries. The SNPs were combined into a 23-plex SNaPshot primer extension assay: Eurasiaplex, designed to complement an existing 34-plex forensic ancestry test with both marker sets occupying well-spaced genomic positions, enabling their combination as single profile submissions to the Bayesian Snipper forensic ancestry inference system. We analyzed the ability of Eurasiaplex plus 34plex SNPs to assign ancestry to a total 1648 profiles from 16 European, 7 Middle East, 13 Central-South Asian and 21 East Asian populations. Ancestry assignment likelihoods were estimated from Snipper using training sets of five-group data (three Eurasian groups, East Asian and African genotypes) and four-group data (Middle East genotypes removed). Five-group differentiations gave assignment success of 91% for NW European populations, 72% for Middle East populations and 39% for Central-South Asian populations, indicating Middle East individuals are not reliably differentiated from either Europeans or Central-South Asians. Four-group differentiations provided markedly improved assignment success rates of 97% for most continental Europeans tested (excluding Turkish and Adygei at the far eastern edge of Europe) and 95% for Central-South Asians, despite applying a probability threshold for the highest likelihood ratio above ‘100 times more likely’. As part of the assessment of the sensitivity of Eurasiaplex to analyze challenging forensic material we detail Eurasiaplex and 34-plex SNP typing to infer ancestry of a cranium recovered from the sea, achieving 82% SNP genotype completeness. Therefore, Eurasiaplex provides an informative and forensically robust approach to the differentiation of European and South Asian ancestries amongst Eurasian populations.     

A mosque-based methadone maintenance treatment strategy: Implementation and pilot results

BackgroundThis paper describes the rationale, implementation and operation of a “world first” Islamic inspired methadone maintenance treatment project delivered in a mosque setting and presents the outcome for the first group of participants. The project explored the viability of expanding addiction recovery services through the network of mosques in Muslim communities.MethodsThe project combined methadone maintenance with peer and religious counseling. Participants consisted of 36 male Muslim heroin users who went through the project. Urine tests and self-reported measures on various dimensions relevant to drug use and quality of life were collected at baseline and 12 months.ResultsThe project had a 12 month retention rate of 80%. At 12 months all but one participant tested negative for opioids and other substances. Self-report measures showed significant reductions in the degree and variety of drug use, improvements in general health, and psychological and social functioning of participants. Qualitative data showed that availability of methadone, convenient location and religion were the main reasons drawing participants to the program.ConclusionsMosques are viable venues for offering medication assisted recovery services and offer an alternative approach for managing addiction in Muslim communities. The prospect of mobilizing community resources to offer community-oriented long-term recovery management programs in mosques and other places of worship deserves consideration.     

Individual level determinants for not receiving immunization,receiving immunization with delay,and being severely underimmunized among rural western Kenyan children

BackgroundEstimating vaccination coverage and delays are important because these measures can identify at risk sub-populations who can be targeted with interventions and public health policies. This paper sought to determine estimates and risk factors for children in rural western Kenya who did not receive immunization, received immunization with delay, or were severely underimmunized.MethodsCaregivers of children aged 12–23 months old were surveyed for immunization history using written records from the immunization booklet. Risk factors for not receiving immunization, delayed immunization, and severe underimmunization were calculated using log-binomial regression. Children were categorized as delayed if a given immunization was received greater than four weeks from the age-appropriate scheduled date. Severely underimmunized children were those who were fully unvaccinated for more than 90 days and had three or more vaccines delayed or not given.ResultsImmunization coverage for pentavalent1, pentavalent3, measles, and fully immunized child (FIC; BCG, three doses of polio, three doses of pentavalent, and measles vaccines) were 99%, 94%, 83%, and 80%, respectively. Approximately, 10%, 24%, and 29%, of children were delayed for pentavalent1, pentavalent3, and measles, respectively. Each model produced a unique combination of risk factors with only advanced maternal age as a risk factor common to all models. Children with delayed receipt of pentavalent1 were at risk for not receiving pentavalent3 (RR: 5.20; 95%CI 3.48, 7.77), measles vaccine (RR: 1.48; 95%CI 1.12, 1.95), and not achieving FIC (RR: 1.88; 95%CI 1.51, 2.34) compared with children who received pentavalent1 on time.ConclusionsImmunization coverage among 12–23 month old children was high, yet a substantial proportion of children were vaccinated with delay. Although vaccine coverage and timeliness are often conceptualized as separate measures, the finding that delayed pentavalent1 receipt was a strong risk factor for not receiving future immunizations indicates the two measures are intertwined.     

Peer victimization,prison climate,resilience and psychological distress of incarcerated juvenile offenders in Ghana: A serial mediation examination

Most Ghanaian research in the area of victimization among children has focused on the school setting. Little research has been done in an attempt to understand inmate-on-inmate victimization within the juvenile correctional facilities in Ghana. This study, therefore, investigated the extent to which peer victimization influences psychological distress among juvenile offenders in the Senior Correctional Center of Ghana. A cross-sectional design was used to purposively sample 115 juvenile offenders for the study. Following mediation analysis performed in PROCESS, the results revealed that prison climate and resilience serially mediated the relationship between peer victimization and psychological distress. Independently, both prison climate and resilience mediated the relationship between peer victimization and psychological distress. It was recommended that anti-bullying programs ought to be institutionalized to create mental health awareness within the correctional facilities. Also, support systems such as the Listener Scheme need to be deployed within the correctional facilities.     

What’s on the bag? The DNA composition of evidence bags pre- and post-exhibit examination

Current forensic DNA profiling kits and techniques enable the detection of trace amounts of DNA. With advancements in kit sensitivity, there is an increased probability of detecting DNA from contamination. Research into DNA transfer within operational forensic laboratories provides insight into the possible mechanisms that may lead to exhibit contamination. To gain a greater understanding of the potential for evidence bags to act as DNA transfer vectors, the level of DNA accumulating on the exterior of evidence bags during the exhibit examination process was investigated. The exterior of 60 evidence bags were tapelifted before and after the examination of the exhibit inside of the bag resulting in 120 DNA profiles. These DNA profiles were compared to DNA profiles of staff working within the building and samples taken from the exhibit inside the bag. Common DNA profile contributors from each sample were also identified through STRmix™ mixture to mixture analysis. The average DNA quantity and number of profile contributors was higher in samples taken from the bag before exhibit examination than after examination. Fifty six percent of all samples taken identified a match between DNA recovered from the evidence bag and at least one staff member. On 11 bags, a common contributor was identified between the exhibit in the bag and the exhibit package post-examination. In one instance a DNA profile, matching that of a donor, on the exhibit bag before examination was also detected on a sample taken from the exhibit, raising the possibility of outer bag-to-exhibit DNA contamination. This study demonstrates that operational forensic laboratories must consider exhibit packages as a potential source of DNA contamination and evaluate their exhibit handling and storage procedures accordingly.     

Exploring tapelifts as a method for dual workflow STR amplification

Although a version of direct PCR is implemented in forensic laboratories for reference material, its incorporation into workflow for the analysis of touch DNA, as a form of latent DNA, from casework exhibits is not. In addition to concerns about increased sensitivity causing more complex mixtures or the generation of more genetic data implicating an individual superfluous to the context of the alleged event, the complete use of the collected sample in the PCR as template has meant that there is no possibility for data reproducibility when needed. Here it is proposed that the use of tapelifts in touch DNA collection can facilitate replicate direct PCR analysis from a single sample allowing the sample to be re-tested. If all portions of the tapelift result in profiles with allelic and likelihood ratio concordance, these sub-samples may be accepted as technical replicates, thus meeting any accreditation guideline requirements. Furthermore, we assess the use of a single tapelift for both direct PCR and extraction-based PCR workflows to illustrate the potential for benefits of both systems to be facilitated. DNA was deposited by three donors onto six substrates with five sample replicates of each condition. Separation of each tapelift into three portions for three direct PCRs ensued using VeriFiler™ Plus. Separation of single tapelifts into three direct PCRs showed no statistical difference in donor allele calls or RFU, or subsequent LRs associated with their profiles. Comparison of profiles within the single tapelift showed more similarity, with high mixture-to-mixture match likelihoods, than when these sub-samples were compared with profiles generated from other samples. This allows each sub-sample taken from the tapelift to be considered as technical replicates. For dual workflow facilitation assessment, one donor deposited DNA through touch onto six substrates with five research replicates of each. Separation of single tapelifts into two portions, one for direct PCR and the retention and use of the remaining portion for extraction and subsequent PCR, showed no significant difference in allelic yield and subsequent donor comparison LRs. Comparison of deconvoluted profiles produced from a single tapelift showed high mixture-to-mixture match likelihoods, supporting DNA donor concordance. This indicates that removing a portion of a tapelift for direct PCR amplification, while processing the remainder through standard processes, allows increased sensitivity through direct PCR while offering the preparation of an eluate suitable for repeated analyses.     

Haplotype distribution in a forensic full mtDNA genome database of admixed Southern Brazilians and its association with self-declared ancestry and pigmentation traits

Background:The advent of massively parallel sequencing (MPS) applications focused on the generation of forensic-quality full mitochondrial genome sequences led to a popularization of the technique on a global scale. However, the lack of forensic-graded population databases has refrained a wider adoption of full genome sequences as the industry standard, despite its better discrimination capacity of individual maternal lineages.Purpose:This work describes a forensic-oriented full mtDNA genome database comprised of 480 samples from a Southern Brazilian population.Methods:A collection of mitochondrial sequences were obtained from low-pass, full genome DNA sequencing results. The complete sample set was evaluated regarding haplotype composition and distribution. Summary statistics and forensic parameters were calculated and are presented for the database, with detailed information concerning the impact of removing genetic information in the form of specific variants or increasingly larger genomic regions. Interpopulational analysis comparing haplotypical diversity in Brazilian and 26 worldwide populations was also performed. The association between mitochondrial genetic variability and phenotypic diversity was also evaluated in populations, with self-declared ancestry and three distinct phenotypic pigmentation traits (eyes, skin and hair colors) as parameters.Results:The presented database can be used to evaluate mitochondrial-related genetic evidence, providing LR values of up to 20,465 for unobserved haplotypes. Haplotype distribution in Southern Brazil seems to be different than the remaining of the country, with a larger contribution of maternal lines with European origin. Despite association can be found between lighter and darker phenotypes or self-declared ancestry and haplotype distribution, prediction models cannot be reliably proposed due to the admixed nature of the Brazilian population.Conclusions:The proposed database provides a basis for statistical calculation and frequency estimation of full mitochondrial genomes, and can be part of an integrated, representative, national database comprising most of the genetic diversity of maternal lineages in the country.     

Ion Torrent ™ Genexus ™ Integrated Sequencer and ForeNGS Analysis Software—An automatic NGS-STR workflow from DNA to profile for forensic science

The Ion Torrent ™ Genexus ™ Sequencer (Genexus) is a highly integrated instrument that can automate library construction, templating, and sequencing in a single-instrument run. By programing the ForeNGS Analysis Software (FNAS), we bridged the gap between sequencing and genotyping without manual intervention. FNAS can automatically transfer sequencing output files from Genexus, analyze the repeat and flanking regions aligned to the GRCh38 assembly, name the alleles according to the ISFG guidelines, and generate user-friendly interactive profiles. Genexus and FNAS can accomplish the fully automatic DNA-to-Profile workflow in forensics. Based on our experiences, the optimal assay parameters on Genexus were validated as follows: 24 cycles of target amplification for library construction; 40 μL of library and 400 bp of template size for templating; 852 flows of dNTPs by order of Ion samba HID2 for sequencing; and 750,000 reads per sample at minimum for 16 samples multiplexed on a lane. By developmental validations of the Precision ID Globalfiler ™ NGS STR Panel v2, Genexus presented competitive performance at the optimal assay parameters qualified to detect commonly used forensic STR markers. It could produce repeatable and reproducible results, and human profiles could be easily separated from nonhuman profiles. Additionally, Genexus was sensitive enough to detect samples with 100 pg of input DNA, and it was suitable for various types of case samples, especially for low copy number samples and degraded samples. Moreover, minor contributors could be detected between the 4:1 and 1:4 mixtures with an analysis threshold of 50 × . The Genexus workflow is a robust and labor-effective solution enabling forensic scientists to obtain NGS-STR profiles within a single day and with only the need to prepare DNA extracts, then set up Genexus, and finally interpret profiles on FNAS.