Thiomicrorhabdus heinhorstiae sp. nov. and Thiomicrorhabdus cannonii sp. nov.: novel sulphur-oxidizing chemolithoautotrophs isolated from the chemocline of Hospital Hole, an anchialine sinkhole in Spring Hill, Florida, USA.

Two sulphur-oxidizing, chemolithoautotrophic aerobes were isolated from the chemocline of an anchialine sinkhole located within the Weeki Wachee River of Florida. Gram-stain-negative cells of both strains were motile, chemotactic rods. Phylogenetic analysis of the 16S rRNA gene and predicted amino acid sequences of ribosomal proteins, average nucleotide identities, and alignment fractions suggest the strains HH1T and HH3T represent novel species belonging to the genus Thiomicrorhabdus. The genome G+C fraction of HH1T is 47.8 mol% with a genome length of 2.61 Mb, whereas HH3T has a G+C fraction of 52.4 mol% and 2.49 Mb genome length. Major fatty acids of the two strains included C16 : 1, C18 : 1 and C16 : 0, with the addition of C10:0 3-OH in HH1T and C12 : 0 in HH3T. Chemolithoautotrophic growth of both strains was supported by elemental sulphur, sulphide, tetrathionate, and thiosulphate, and HH1T was also able to use molecular hydrogen. Neither strain was capable of heterotrophic growth or use of nitrate as a terminal electron acceptor. Strain HH1T grew from pH 6.5 to 8.5, with an optimum of pH 7.4, whereas strain HH3T grew from pH 6 to 8 with an optimum of pH 7.5. Growth was observed between 15-35 °C with optima of 32.8 °C for HH1T and 32 °C for HH3T. HH1T grew in media with [NaCl] 80-689 mM, with an optimum of 400 mM, while HH3T grew at 80-517 mM, with an optimum of 80 mM. The name Thiomicrorhabdus heinhorstiae sp. nov. is proposed, and the type strain is HH1T (=DSM 111584T=ATCC TSD-240T). The name Thiomicrorhabdus cannonii sp. nov is proposed, and the type strain is HH3T (=DSM 111593T=ATCC TSD-241T).

MIRRORS program: Helping pregnant and postpartum women and families with substance use problems.

Background: Pregnant and postpartum women with substance use disorders are a highly vulnerable population, especially when this is compounded by homelessness or unstable housing, justice involvement, and/or co-occurring mental health challenges. The MIRRORS (Maternal Initiative for Reflective Recovery-Oriented Residential Services) program provided expanded and enhanced residential substance use disorder treatment, prevention and recovery support for women and children through integrated, trauma-informed care and services strengthened by a comprehensive and coordinated family systems approach. This paper describes the program and provides evaluation of the outcomes. Methods: Pregnant and postpartum women (n = 215) were assessed at 3 time points: intake, discharge and 6-months post-intake using standardized measures of family functioning, parenting, recovery capital, and other outcomes. Multilevel modeling was employed to examine individual differences in trends over time. Results: Over 80% of participants reported that the MIRRORS program enhanced their recovery treatment experience. Women reported significant improvements in general family functioning, problem solving, behavioral control, affective responsiveness, and communication. Participants also reported increased recovery capital and improved parental monitoring over time. Conclusions: Outcomes indicate that the MIRRORS program was effective in improving family functioning and reducing substance use, thus enhancing women's functioning and recovery.

Evolution of Sequence Type 4821 Clonal Complex Hyperinvasive and Quinolone-Resistant Meningococci.

Expansion of quinolone-resistant Neisseria meningitidis clone ChinaCC4821-R1-C/B from sequence type (ST) 4821 clonal complex (CC4821) caused a serogroup shift from serogroup A to serogroup C invasive meningococcal disease (IMD) in China. To determine the relationship among globally distributed CC4821 meningococci, we analyzed whole-genome sequence data from 173 CC4821 meningococci isolated from 4 continents during 1972-2019. These meningococci clustered into 4 sublineages (1-4); sublineage 1 primarily comprised of IMD isolates (41/50, 82%). Most isolates from outside China (40/49, 81.6%) formed a distinct sublineage, the Europe-USA cluster, with the typical strain designation B:P1.17-6,23:F3-36:ST-3200(CC4821), harboring mutations in penicillin-binding protein 2. These data show that the quinolone-resistant clone ChinaCC4821-R1-C/B has expanded to other countries. The increasing distribution worldwide of serogroup B CC4821 raises the concern that CC4821 has the potential to cause a pandemic that would be challenging to control, despite indirect evidence that the Trumenba vaccine might afford some protection.

Screening Programs for SARS-CoV-2 Infections on a University Campus - Austin, Texas, September 30-November 30, 2020.

Colleges and universities in the United States have relied on various measures during the COVID-19 pandemic to prevent transmission of SARS-CoV-2, the virus that causes COVID-19, including implementing testing programs (1-3). These programs have permitted a safer return to campus for students by identifying infected persons and temporarily isolating them from the campus population (2,3). The University of Texas at Austin (UT Austin) implemented COVID-19 prevention measures in Fall 2020* including the following testing programs: clinic-based diagnostic testing, voluntary community screening, and targeted screening (testing of specific student populations in situations of increased transmission risk). During September 30-November 30, 2020, UT Austin students participated in tests for SARS-CoV-2, which resulted in the detection of 401 unique student cases of COVID-19 from among 32,401 tests conducted.† Among students who participated in one targeted screening program for students attending campus events, 18 (37.5%) of 48 infected students were asymptomatic at the time of their positive test result compared with 45 (23%) of 195 students identified through community testing and nine (5.8%) of 158 students identified through clinic-based testing. Targeted screening also identified a different population of students than did clinic-based and community testing programs. Infected students tested through targeted screening were more likely to be non-Hispanic White persons (chi square = 20.42; p<0.03), less likely to engage in public health measures, and more likely to have had interactions in settings where the risk for SARS-CoV-2 transmission is higher, such as restaurants, gyms, and residence halls. In addition to clinic-based SARS-CoV-2 testing at colleges and universities, complementary testing programs such as community and targeted screening might enhance efforts to identify and control SARS-CoV-2 transmission, especially among asymptomatic persons and disproportionately affected populations that might not otherwise be reached.

Walking cadence required to elicit criterion moderate-intensity physical activity is moderated by fitness status.

The aims of this study were to estimate the walking cadence required to elicit a VO2reserve (VO2R) of 40% and determine if fitness status moderates the relationship between walking cadence and %VO2R. Twenty participants (10 male, mean(s) age 32(10) years; VO2max 45(10) mL·kg-1·min-1) completed resting and maximal oxygen consumption tests prior to 7 x 5-min bouts of treadmill walking at increasing speed while wearing an Apple Watch and measuring oxygen consumption continuously. The 7 x 5-min exercise bouts were performed at speeds between 3 and 6 km·h-1 with 5-min seated rest following each bout. Walking cadence measured at each treadmill speed was recorded using the Apple Watch "Activity" app. Using Bayesian regression, we predict that participants need a walking cadence of 138 to 140 steps·min-1 to achieve a VO2R of 40%. However, these values are moderated by fitness status such that those with lower fitness can achieve 40% VO2R at a slower walking cadence. The results suggest that those with moderate fitness need to walk at ~40% higher than the currently recommended walking cadence (100 steps·min-1) to elicit moderate-intensity physical activity. However, walking cadence required to achieve moderate-intensity physical activity is moderated by fitness status.

Heavy Metal Susceptibility of Escherichia coli Isolated from Urine Samples from Sweden, Germany, and Spain.

Antimicrobial resistance is a major health care problem, with the intensive use of heavy metals and biocides recently identified as a potential factor contributing to the aggravation of this situation. The present study investigated heavy metal susceptibility and genetic resistance determinants in Escherichia coli isolated from clinical urine samples from Sweden, Germany, and Spain. A total of 186 isolates were tested for their sodium arsenite, silver nitrate, and copper(II) sulfate MICs. In addition, 88 of these isolates were subjected to whole-genome sequencing for characterization of their genetic resistance determinants and epidemiology. For sodium arsenite, the isolates could be categorized into a resistant and a nonresistant group based on MIC values. Isolates of the resistant group exhibited the chromosomal ars operon and belonged to non-B2 phylogenetic groups; in contrast, within the B2 phylogroup, no ars operon was found, and the isolates were susceptible to sodium arsenite. Two isolates also harbored the silver/copper resistance determinant pco/sil, and they belonged to sequence types ST10 (phylogroup A) and ST295 (phylogroup C). The ST295 isolate had a silver nitrate MIC of ≥512 mg/liter and additionally produced extended-spectrum beta-lactamases. To our knowledge, this is the first study to describe the distribution of the arsenic resistance ars operon within phylogroups of E. coli strains isolated from patients with urinary tract infections. The arsenic resistance ars operon was present only in all non-B2 clades, which have previously been associated with the environment and commensalism in both humans and animals, while B2 clades lacked the ars operon.

Diversity and distribution of nuclease bacteriocins in bacterial genomes revealed using Hidden Markov Models.

Bacteria exploit an arsenal of antimicrobial peptides and proteins to compete with each other. Three main competition systems have been described: type six secretion systems (T6SS); contact dependent inhibition (CDI); and bacteriocins. Unlike T6SS and CDI systems, bacteriocins do not require contact between bacteria but are diffusible toxins released into the environment. Identified almost a century ago, our understanding of bacteriocin distribution and prevalence in bacterial populations remains poor. In the case of protein bacteriocins, this is because of high levels of sequence diversity and difficulties in distinguishing their killing domains from those of other competition systems. Here, we develop a robust bioinformatics pipeline exploiting Hidden Markov Models for the identification of nuclease bacteriocins (NBs) in bacteria of which, to-date, only a handful are known. NBs are large (>60 kDa) toxins that target nucleic acids (DNA, tRNA or rRNA) in the cytoplasm of susceptible bacteria, usually closely related to the producing organism. We identified >3000 NB genes located on plasmids or on the chromosome from 53 bacterial species distributed across different ecological niches, including human, animals, plants, and the environment. A newly identified NB predicted to be specific for Pseudomonas aeruginosa (pyocin Sn) was produced and shown to kill P. aeruginosa thereby validating our pipeline. Intriguingly, while the genes encoding the machinery needed for NB translocation across the cell envelope are widespread in Gram-negative bacteria, NBs are found exclusively in γ-proteobacteria. Similarity network analysis demonstrated that NBs fall into eight groups each with a distinct arrangement of protein domains involved in import. The only structural feature conserved across all groups was a sequence motif critical for cell-killing that is generally not found in bacteriocins targeting the periplasm, implying a specific role in translocating the nuclease to the cytoplasm. Finally, we demonstrate a significant association between nuclease colicins, NBs specific for Escherichia coli, and virulence factors, suggesting NBs play a role in infection processes, most likely by enabling pathogens to outcompete commensal bacteria.

The validity and inter-device variability of the Apple Watch™ for measuring maximal heart rate.

Maximal heart rate (HRmax) is a fundamental measure used in exercise prescription. The Apple Watch™ measures heart rate yet the validity and inter-device variability of the device for measuring HRmax are unknown. Fifteen participants completed a maximal oxygen uptake test while wearing an Apple Watch™ on each wrist. Criterion HRmax was measured using a Polar T31™ chest strap. There were good to very good correlations between the watches and criterion (left: r = 0.87 [90%CI: 0.67 to 0.95]; right: r = 0.98 [90%CI: 0.94 to 0.99]). Standardised mean bias for the left and right watches compared to the criterion were 0.14 (90%CI: -0.12 to 0.39; trivial) and 0.04 (90%CI: -0.07 to 0.15; trivial). Standardised typical error of the estimate for the left and right watches compared to the criterion were 0.51 (90%CI: 0.38 to 0.80; moderate) and 0.22 (90%CI: 0.16 to 0.34; small). Inter-device standardised typical error was 0.46 (90%CI: 0.36 to 0.68; moderate), ICC = 0.84 (90%CI: 0.65 to 0.93). The Apple Watch™ has good to very good criterion validity for measuring HRmax, with no substantial under- or over-estimation. There were moderate and small prediction errors for the left and right watches. Inter-device variability in HRmax is moderate.

Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad.

BACKGROUND: Serogroup A Neisseria meningitidis (NmA) was the cause of the 2011 meningitis epidemics in Chad. This bacterium, often carried asymptomatically, is considered to be an "accidental pathogen"; however, the transition from carriage to disease phenotype remains poorly understood. This study examined the role genetic diversity might play in this transition by comparing genomes from geographically and temporally matched invasive and carried NmA isolates. RESULTS: All 23 NmA isolates belonged to the ST-5 clonal complex (cc5). Ribosomal MLST comparison with other publically available NmA:cc5 showed that isolates were closely related, although those from Chad formed two distinct branches and did not cluster with other NmA, based on their MLST profile, geographical and temporal location. Whole genome MLST (wgMLST) comparison identified 242 variable genes among all Chadian isolates and clustered them into three distinct phylogenetic groups (Clusters 1, 2, and 3): no systematic clustering by disease or carriage source was observed. There was a significant difference (p = 0.0070) between the mean age of the individuals from which isolates from Cluster 1 and Cluster 2 were obtained, irrespective of whether the person was a case or a carrier. CONCLUSIONS: Whole genome sequencing provided high-resolution characterization of the genetic diversity of these closely related NmA isolates. The invasive meningococcal isolates obtained during the epidemic were not homogeneous; rather, a variety of closely related but distinct clones were circulating in the human population with some clones preferentially colonizing specific age groups, reflecting a potential age-related niche adaptation. Systematic genetic differences were not identified between carriage and disease isolates consistent with invasive meningococcal disease being a multi-factorial event resulting from changes in host-pathogen interactions along with the bacterium.

Clonal Expansion of New Penicillin-Resistant Clade of Neisseria meningitidis Serogroup W Clonal Complex 11, Australia.

In Western Australia, Neisseria meningitidis serogroup W clonal complex 11 became the predominant cause of invasive meningococcal disease in 2016. We used core-genome analysis to show emergence of a penicillin-resistant clade that had the penA_253 allele. This new penicillin-resistant clade might affect treatment regimens for this disease.

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork.

Campylobacter jejuni is a major cause of bacterial gastroenteritis worldwide, primarily associated with the consumption of contaminated poultry. C. jejuni lineages vary in host range and prevalence in human infection, suggesting differences in survival throughout the poultry processing chain. From 7343 MLST-characterised isolates, we sequenced 600 C. jejuni and C. coli isolates from various stages of poultry processing and clinical cases. A genome-wide association study (GWAS) in C. jejuni ST-21 and ST-45 complexes identified genetic elements over-represented in clinical isolates that increased in frequency throughout the poultry processing chain. Disease-associated SNPs were distinct in these complexes, sometimes organised in haplotype blocks. The function of genes containing associated elements was investigated, demonstrating roles for cj1377c in formate metabolism, nuoK in aerobic survival and oxidative respiration, and cj1368-70 in nucleotide salvage. This work demonstrates the utility of GWAS for investigating transmission in natural zoonotic pathogen populations and provides evidence that major C. jejuni lineages have distinct genotypes associated with survival, within the host specific niche, from farm to fork.

Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates.

Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods. Whole-genome sequencing (WGS) data enable the improvement of sequence-based typing approaches, such as multilocus sequence typing (MLST), by substantially increasing the number of loci examined. A core genome MLST (cgMLST) scheme defines a comprehensive set of those loci present in most members of a bacterial group, balancing very high resolution with comparability across the diversity of the group. Here we propose a set of 1,343 loci as a human campylobacteriosis cgMLST scheme (v1.0), the allelic profiles of which can be assigned to core genome sequence types. The 1,343 loci chosen were a subset of the 1,643 loci identified in the reannotation of the genome sequence of C. jejuni isolate NCTC 11168, chosen as being present in >95% of draft genomes of 2,472 representative United Kingdom campylobacteriosis isolates, comprising 2,207 (89.3%) C. jejuni isolates and 265 (10.7%) C. coli isolates. Validation of the cgMLST scheme was undertaken with 1,478 further high-quality draft genomes, containing 150 or fewer contiguous sequences, from disease isolate collections: 99.5% of these isolates contained ≥95% of the 1,343 cgMLST loci. In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak.

Development and evaluation of two instruments for assessing screening, brief intervention, and referral to treatment (SBIRT) competency.

BACKGROUND: Screening, brief intervention, and referral to treatment (SBIRT) is shown to be effective in identifying, intervening with, and making appropriate referrals for patients with unhealthy alcohol use. SBIRT training consists of knowledge-based and skill-based components and has increased the use of screening and intervention skills in clinical settings. This article reports on the development and evaluation of 2 SBIRT proficiency checklists for use across institutions to assess SBIRT skills in both simulated and clinical encounters. METHODS: A national panel of 16 experts identified 137 discrete SBIRT skills items for the checklists. From this final list, 2 proficiency checklists were derived: the SBIRT Proficiency Checklist (SPC), composed of 22 questions for videotaped interviews, and the Clinical SBIRT Proficiency Checklist (CSPC), composed of 13 questions for direct clinical observation. An evaluation was conducted to test the reliability of the SPC and to assess the utility of the CSPC. RESULTS: Two checklists for assessing SBIRT proficiency were developed by a collaborative workgroup. Fleiss' kappa analyses indicated moderate agreement. In addition, faculty recorded satisfaction with the CSPC for assessing residents on their SBIRT performance during clinical encounters. CONCLUSIONS: The SPC and the CSPC are practical tools for assessing competence with SBIRT and are easily integrated as standard instruments in a wide range of training settings. Future advancements to the checklists and their evaluation include modification of the SPC rating scale to be consistent with the CSPC, developing a training program for using the checklists, and further testing to improve interrater reliability.

Resolution of a Protracted Serogroup B Meningococcal Outbreak with Whole-Genome Sequencing Shows Interspecies Genetic Transfer.

A carriage study was undertaken (n = 112) to ascertain the prevalence of Neisseria spp. following the eighth case of invasive meningococcal disease in young children (5 to 46 months) and members of a large extended indigenous ethnic minority Traveller family (n = 123), typically associated with high-occupancy living conditions. Nested multilocus sequence typing (MLST) was employed for case specimen extracts. Isolates were genome sequenced and then were assembled de novo and deposited into the Bacterial Isolate Genome Sequencing Database (BIGSdb). This facilitated an expanded MLST approach utilizing large numbers of loci for isolate characterization and discrimination. A rare sequence type, ST-6697, predominated in disease specimens and isolates that were carried (n = 8/14), persisting for at least 44 months, likely driven by the high population density of houses (n = 67/112) and trailers (n = 45/112). Carriage for Neisseria meningitidis (P < 0.05) and Neisseria lactamica (P < 0.002) (2-sided Fisher's exact test) was more likely in the smaller, more densely populated trailers. Meningococcal carriage was highest in 24- to 39-year-olds (45%, n = 9/20). Evidence of horizontal gene transfer (HGT) was observed in four individuals cocolonized by Neisseria lactamica and Neisseria meningitidis One HGT event resulted in the acquisition of 26 consecutive N. lactamica alleles. This study demonstrates how housing density can drive meningococcal transmission and carriage, which likely facilitated the persistence of ST-6697 and prolonged the outbreak. Whole-genome MLST effectively distinguished between highly similar outbreak strain isolates, including those isolated from person-to-person transmission, and also highlighted how a few HGT events can distort the true phylogenetic relationship between highly similar clonal isolates.

Genomics Reveals the Worldwide Distribution of Multidrug-Resistant Serotype 6E Pneumococci.

The pneumococcus is a leading pathogen infecting children and adults. Safe, effective vaccines exist, and they work by inducing antibodies to the polysaccharide capsule (unique for each serotype) that surrounds the cell; however, current vaccines are limited by the fact that only a few of the nearly 100 antigenically distinct serotypes are included in the formulations. Within the serotypes, serogroup 6 pneumococci are a frequent cause of serious disease and common colonizers of the nasopharynx in children. Serotype 6E was first reported in 2004 but was thought to be rare; however, we and others have detected serotype 6E among recent pneumococcal collections. Therefore, we analyzed a diverse data set of ∼1,000 serogroup 6 genomes, assessed the prevalence and distribution of serotype 6E, analyzed the genetic diversity among serogroup 6 pneumococci, and investigated whether pneumococcal conjugate vaccine-induced serotype 6A and 6B antibodies mediate the killing of serotype 6E pneumococci. We found that 43% of all genomes were of serotype 6E, and they were recovered worldwide from healthy children and patients of all ages with pneumococcal disease. Four genetic lineages, three of which were multidrug resistant, described ∼90% of the serotype 6E pneumococci. Serological assays demonstrated that vaccine-induced serotype 6B antibodies were able to elicit killing of serotype 6E pneumococci. We also revealed three major genetic clusters of serotype 6A capsular sequences, discovered a new hybrid 6C/6E serotype, and identified 44 examples of serotype switching. Therefore, while vaccines appear to offer protection against serotype 6E, genetic variants may reduce vaccine efficacy in the longer term because of the emergence of serotypes that can evade vaccine-induced immunity.

Defining the estimated core genome of bacterial populations using a Bayesian decision model.

The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance.

Impact Evaluation of an After-school Cooking Skills Program in a Disadvantaged Community: Back to Basics.

PURPOSE: Few efficacious child obesity interventions have been converted into ongoing community programs in the after-school setting. The aim of this study was to evaluate the impact of phase 2 of the Back to Basics cooking club on dietary behaviours and fruit and vegetable variety in a population at risk of obesity at a low income school with > 10% indigenous population. METHODS: Baseline and 3-month dietary intake and social cognitive theory (SCT) constructs were collected in 51 children, mean age 9 years, 61% female. McNemar tests were used for comparison of proportions between categorical variables. Cohen's d was used to compare effect sizes across different measures. RESULTS: Consumption of one or more fruit servings per day significantly increased from 41% to 67% (P = 0.02, d = 0.13) and there was a trend for increasing the weekly variety of fruit and vegetables. The SCT constructs assessed within the current study improved significantly (P < 0.05), with moderate to large effect sizes (d = 0.33-0.78). CONCLUSION: This study documents that a previous efficacious healthy lifestyle program can be adapted for use as an obesity prevention program addressing improvements in vegetable and fruit intakes in a low income community with a relatively high indigenous population.

Baylor Pediatric SBIRT Medical Residency Training Program: model description and evaluation.

BACKGROUND: The Baylor College of Medicine SBIRT Medical Residency Training Program is a multilevel project that trains residents and faculty in evidenced-based screening, brief intervention, and referral to treatment methods for alcohol and substance use problems. METHODS: This paper describes the training program created for pediatric residents and provides an evaluation of the program. Ninety-five first-year pediatric residents participated in the training program. They were assessed on satisfaction with the program, self-rated skills, observed competency, and implementation into clinical practice. RESULTS: The program was successfully incorporated into the residency curricula in two pediatric residencies. Evaluations indicate a high degree of satisfaction with the program, self-reported improvement in SBIRT skills, observed proficiency in SBIRT skills, and utilization of SBIRT skills in clinical practice. CONCLUSIONS: SBIRT skills training can be incorporated into pediatric residency training, and residents are able to learn and implement the skills in clinical practice.

Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus.

Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants <12 months in Spain, the UK, and the Netherlands during 2017-20. We show, using targeted metagenomic sequencing of >100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03-9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity.