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HCV active infection can be accurately detected by assays that utilize point-of-care testing or dried blood spot samples for the determination of HCV RNA. Background Finger-stick point-of-care and dried blood spot (DBS) hepatitis C virus (HCV) RNA testing increases testing uptake and linkage to care. This systematic review evaluated the diagnostic accuracy of point-of-care testing and DBS to detect HCV RNA. Methods Bibliographic databases and conference presentations were searched for eligible studies. Meta-analysis was used to pool estimates. Results Of 359 articles identified, 43 studies were eligible and included. When comparing the Xpert HCV Viral Load Fingerstick assay to venous blood samples (7 studies with 987 samples), the sensitivity and specificity for HCV RNA detection was 99% (95% confidence interval [CI], 97%-99%) and 99% (95% CI, 94%-100%) and for HCV RNA quantification was 100% (95% CI, 93%-100%) and 100% (95% CI, 94%-100%). The proportion of invalid results following Xpert HCV Viral Load Fingerstick testing was 6% (95% CI, 3%-11%). When comparing DBS to venous blood samples (28 studies with 3988 samples) the sensitivity and specificity for HCV RNA detection was 97% (95% CI, 95%-98%) and 100% (95% CI, 98%-100%) and for HCV RNA quantification was 98% (95% CI, 96%-99%) and 100% (95% CI, 95%-100%). Conclusions Excellent diagnostic accuracy was observed across assays for detection of HCV RNA from finger-stick and DBS samples. The proportion of invalid results following Xpert HCV Viral Load Fingerstick testing highlights the importance of operator training and quality assurance programs.

Early detection of pathogen cross-transmission events and environmental reservoirs is needed to control derived nosocomial outbreaks. Whole-genome sequencing (WGS) is considered the gold standard for outbreak confirmation, but, in most cases, it is time-consuming and has elevated costs. Consequently, the timely incorporation of WGS results to conventional epidemiology (CE) investigations for rapid outbreak detection is scarce. Fourier transform infrared spectroscopy (FTIR) is a rapid technique that establishes similarity among bacteria based on the comparison of infrared light absorption patterns of bacterial polysaccharides and has been used as a typing tool in recent studies. The aim of the present study was to evaluate the performance of the FTIR as a first-line typing tool for the identification of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-Kp) outbreaks in the hospital setting in comparison with CE investigations using WGS as the gold standard method. Sixty-three isolates of ESBL-Kp collected from 2018 to 2021 and classified according to CE were typed by both FTIR and WGS. Concordance was measured using the Adjusted Rand index (AR) and the Adjusted Wallace coefficient (AW) for both CE and FTIR clustering considering WGS as the reference method. Both AR and AW were significantly higher for FTIR clustering than CE clustering (0.475 vs. 0.134, p = 0.01, and 0.521 vs. 0.134, p = 0.009, respectively). Accordingly, FTIR inferred more true clustering relationships than CE (38/42 vs. 24/42, p = 0.001). However, a similar proportion of genomic singletons was detected by both FTIR and CE (13/21 vs. 12/21, p = 1). This study demonstrates the utility of the FTIR method as a quick, low-cost, first-line tool for the detection of ESBL-Kp outbreaks, while WGS analyses are being performed for outbreak confirmation and isolate characterization. Thus, clinical microbiology laboratories would benefit from integrating the FTIR method into CE investigations for infection control measures in the hospital setting.

Background and Aims Pakistani migrants in Catalonia, Spain, could have high hepatitis C virus (HCV) prevalence. The aims of the HepClink study were (i) to implement and assess the quality of a micro-elimination strategy based on a community intervention and (ii) to obtain data from primary care (PC) registries as a baseline comparator. Methods The community intervention targeted Pakistani adults and consisted of education, screening and simplified access to treatment. Quality indicators were calculated (effectiveness, impact and acceptability). The testing rate, the prevalence of HCV antibodies and HCV-RNA were compared with those observed in the Pakistani population accessing PC in the previous year. Results A total of 505 participants were recruited through the community intervention (64.6% men, median 37 years) vs those accessing PC (N = 25 455, 70.9% men, median 38 years). Among study participants, 35.1% did not know about HCV and 9.7% had been previously tested. The testing rate in the community intervention was 99.4% vs 50.7% in PC. Prevalence was 4.6% vs 7.1% (p = .008) for HCV antibodies and 1.4% (3/6 new diagnoses) vs 2.4% (p = .183) for HCV-RNA. Among the six viremic patients, three began treatment within the intervention and two through the usual circuit and all completed the full course. Conclusions This novel community intervention was well accepted and effective at reaching a Pakistani migrant population with a low-level knowledge of HCV and largely not tested before. The observed prevalence and the high unawareness of their HCV status justify a targeted screening in this group both in the community and in PC.

The coronavirus disease 2019 (COVID-19) pandemic has affected the world radically since 2020. Spain was one of the European countries with the highest incidence during the first wave. As a part of a consortium to monitor and study the evolution of the epidemic, we sequenced 2,170 samples, diagnosed mostly before lockdown measures. Here, we identified at least 500 introductions from multiple international sources and documented the early rise of two dominant Spanish epidemic clades (SECs), probably amplified by superspreading events. Both SECs were related closely to the initial Asian variants of SARS-CoV-2 and spread widely across Spain. We inferred a substantial reduction in the effective reproductive number of both SECs due to public-health interventions (R-e < 1), also reflected in the replacement of SECs by a new variant over the summer of 2020. In summary, we reveal a notable difference in the initial genetic makeup of SARS-CoV-2 in Spain compared with other European countries and show evidence to support the effectiveness of lockdown measures in controlling virus spread, even for the most successful genetic variants. Analysis of 2,170 SARS-CoV-2 sequences from the first wave of the COVID-19 epidemic in Spain provides insights into transmission patterns and the effects of lockdown on the emergence of new variants.

Background: This study aimed to describe the HCV cascade of care among people who inject drugs (PWID) in Catalonia, as well as to compare the observed gaps in care between Spanish-born and migrant PWID. Methods: A cross-sectional study of PWID (N = 410) attending four harm reduction services (HRS) was performed in 2016-17 (HepC detect II Study). Participants were tested for both HCV antibodies (rapid testing) and RNA (from dried blood spot samples). The HCV care cascade was estimated from HCV testing results combined with self-reported data on previous testing, diagnosis and treatment collected through a questionnaire. Logistic regressions were used to test for an association between migration status and the proportions observed in each step of the HCV care cascade adjusting for age, sex, years of injection, homelessness, and treatment for drug dependence. Results: Overall, 85.4% were men and 28.0% were migrants. Among Spanish-born (n = 295) and migrant (n = 115) PWID participants in the study, 96.6% vs. 88.6% had previously been HCV screened (AOR=3.11; 95% CI: 1.11-8.65), 79.3% vs. 80.9% were antibody positive, and 70.7% vs. 67.6% were HCV-RNA positive or cured with treatment; among the latter, 36.6% vs. 18.2% had started treatment (AOR=2.41; 95% CI: 1.09-5.34), and 20.6% vs. 9.1% had been cured by treatment, respectively. Unawareness of having hepatitis C was more common among migrants than Spanish-born PWID (46.0% and 31.5%, respectively; p

Background Containment policies and other restrictions introduced by the Spanish government in response to the COVID-19 pandemic present challenges for marginalised populations, such as people who use drugs. Harm reduction centres are often linked to social services, mental health services, and infectious disease testing, in addition to tools and services that help to reduce the harms associated with injecting drugs. This study aimed to explore the impact of the pandemic on these services in four autonomous communities in Spain. Methods This is a cross-sectional study that employed a seven-section structured survey administered electronically to 20 centres in July 2020. Data from the most heavily affected months (March-June) in 2020 were compared to data from the same period in 2019. Averages were calculated with their ranges, rates, and absolute numbers. Results All 11 responding centres reported having had to adapt or modify their services during the Spanish state of alarm (14 March-21 June 2020). One centre reported complete closure for 2 months and four reported increases in their operating hours. The average number of service users across all centres decreased by 22% in comparison to the same period in the previous year and the average needle distribution decreased by 40% in comparison to 2019. Most centres reported a decrease in infectious disease testing rates (hepatitis B and C viruses, human immunodeficiency virus, and tuberculosis) for March, April, and May in 2020 compared to the previous year. Reported deaths as a result of overdose did not increase during the state of alarm, but 2/11 (18%) centres reported an increase in overdose deaths immediately after finalisation of the state of alarm. Conclusion Overall, Spanish harm reduction centres were able to continue operating and offering services by adjusting operating hours. The number of overall service users and needles distributed fell during the Spanish state of alarm lockdown period, suggesting that fewer clients accessed harm reduction services during this time, putting them at greater risk of reusing or sharing injecting equipment, overdosing, acquiring infectious diseases with decreased access to testing or discontinuing ongoing treatment such as methadone maintenance therapy, hepatitis C treatment, or antiretroviral therapy.

Background: In Catalonia (Spain), people who inject drugs (PWID) face numerous barriers to access to mainstream healthcare services for hepatitis C confirmatory diagnosis and treatment, so simplified testing strategies for viremic infection are urgently needed. Among PWID attending harm-reduction services in Catalonia, we aimed (i) to assess the utility of an in-house HCV-RNA detection assay on dried blood spots (DBS) as a one-step screening and confirmatory diagnosis strategy for hepatitis C, (ii) to estimate the prevalence of viremic HCV infection, and (iii) to identify factors associated with unawareness of viremic infection. Methods: A cross-sectional study of current PWID (N = 410) was performed in four harm-reduction services. All participants underwent HCV antibody point-of-care testing and parallel DBS collection for centralized RNA testing. An epidemiological questionnaire was administered. Paired EDTA-plasma samples were additionally collected for HCV viral load testing in 300 participants. Results: HCV-RNA testing from DBS was feasible and showed 97.2% sensitivity and 100% specificity for viral loads > 3000 IU/mL in real-life conditions. No significant differences in the performance when detecting viremic infections were observed between this one-step testing strategy vs. the conventional two-step algorithm involving venepuncture. Overall HCV seroprevalence was 79.8%, and prevalence of viremic infection was 58.5%. Importantly, 35.8% of viremic HCV participants were unaware of their status, and no specific socio-demographic or bio-behavioral factors independently associated with unawareness of viremic infection were identified. Among participants reporting a past or current HCV infection, 29.0% stated having received HCV antiviral treatment. Conclusion: The high viremic HCV infection burden among PWID attending HRS, estimated for the first time in Catalonia, together with the low levels of awareness of viremic status and access to treatment, suggest that scaling up this one-step screening and diagnosis strategy to the network of harm-reduction services would help to achieve HCV elimination targets set by the World Health Organization.

Alternative strategies are required to enhance the diagnosis of silent hepatitis C virus (HCV) infections in key populations at risk. Among them, HCV prevalence and bio-behavioural data are scarce for HIV-negative men who have sex with men (MSM) and men and trans-women sex workers. We sought to describe and assess the potential benefits of a community-based one-step HCV screening and confirmatory strategy for these populations in Barcelona. The screening strategy based on a real-time RT-PCR assay for HCV-RNA detection in dried-blood spots (DBS) was validated and implemented in addition to an antibody point-of-care test in a community centre. HCV prevalence was assessed, and bio-behavioural data were collected. The molecular assay was precise, reproducible, sensitive and specific. Four HIV-negative MSM reported being currently infected (0.75% HCV self-reported prevalence). Implementation of DBS testing was easy, and acceptability was >95%, but no silent HCV case was diagnosed (N=580). High-risk sexual practices and drug use for sex were reported frequently. HIV prevalence was 4.7% in MSM and 10% in sex workers. Self-reported prevalence of other STIs ranged from 11.3% to 36.2%. In conclusion, HCV-RNA testing in DBS showed a good performance, but the assessed one-step strategy does not seem beneficial in this setting. Although no silent HCV infections were detected, the observed high-risk behaviours and prevalence of other STIs suggest that HCV spread should be periodically monitored among these populations in Barcelona by means of behavioural surveillance, rapid antibody testing and molecular confirmation in DBS.

Objectives: Onco-haematological patients are prone to develop infections, and antibiotic prophylaxis may lead to negative blood cultures. Thus, the microbiological diagnosis and subsequent administration of a targeted antimicrobial therapy is often difficult. The goal of this study was to evaluate the usefulness of IRIDICA (PCR/ESI-MS technology) for the molecular diagnosis of bloodstream infections in this patient group. Methods: A total of 463 whole blood specimens from different sepsis episodes in 429 patients were analysed using the PCR/ESI-MS platform, comparing the results with those of blood culture and other clinically relevant information. Results: The sensitivity of PCR/ESI-MS by specimen (excluding polymicrobial infections, n Z 25) in comparison with blood culture was 64.3% overall, 69.0% in oncological patients, and 59.3% in haematological patients. When comparing with a clinical infection criterion, overall sensitivity rose to 74.7%, being higher in oncological patients (80.0%) than in haematological patients (67.7%). Thirty-one microorganisms isolated by culture were not detected by IRIDICA, whereas 42 clinically relevant pathogens not isolated by culture were detected moleculary. Conclusions: PCR/ESI-MS offers a reliable identification of pathogens directly from whole blood. While additional studies are needed to confirm our findings, the system showed a lower sensitivity in onco-haematological patients in comparison with previously reported results in patients from the Intensive Care Unit. (C) 2016 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Half of the patients chronically infected with hepatitis C virus (HCV) genotype 1 fail to respond to pegylated interferon alpha (PEG-IFN) and ribavirin (RBV) therapy. This study assesses the effects of treatment on the evolution of the E1-E2 viral region in non-responder patients infected with HCV-1b. Twenty-three HCV-1b chronically infected patients were studied retrospectively, including 19 non-responders to PEG-IFN/RBV therapy (11 null-responders and 8 relapsers) in the study group, and 4 untreated patients in the control group. Genetic and phylogenetic analyses of the E1-E2 viral populations were performed at baseline and at the time of treatment failure to assess changes in genetic variability and evolutionary dynamics during treatment. Baseline virological characteristics were similar in null-responders, relapsers and controls. E1-E2 genetic variability decreased during treatment in non-responders, with a more pronounced decline in relapsers than in null-responders. A specific evolutionary pattern was not observed in null-responders, while a complete substitution of viral variants found at baseline characterised relapser patients. No specific E1-E2 amino acid substitution involved in treatment failure could be identified. In conclusion, although diverse evolutionary patterns with no apparent common adaptive changes were observed during therapy, treatment failure was characterised by a decline in genetic diversity. (C) 2012 Elsevier B.V. All rights reserved.

Background: Quantification and description of patients recently infected by HIV can provide an accurate estimate of the dynamics of HIV transmission. Between 2006 and 2008 in Catalonia, we estimated the prevalence of recent HIV infection among newly diagnosed cases, described the epidemiological characteristics of the infection according to whether it was recent, long-standing or advanced, and identified factors associated with recent infection. Methods: A Test for Recent Infection (TRI) was performed in serum samples from patients newly diagnosed with HIV. Two different TRI were used: the Vironostika-LS assay (January 2006-May 2007) and the BED-CEIA CEIA (June 2007 onwards). Samples were obtained within the first 6 months of diagnosis. Patients whose samples tested positive in the TRI were considered recently infected. Results: Of 1125 newly diagnosed patients, 79.9% were men (median age, 35.4 years), 38.7% were born outside Spain, 48.9% were men who have sex with men (MSM) and 10.6% presented other sexually transmitted infections. The overall percentage of recent infection was 23.0%, which increased significantly, from 18.1% in 2006 to 26.2% in 2008. This percentage was higher for patients from South America (27.6%). Factors associated with recent infection were acquiring infection through sexual contact between MSM [odds ratio (OR) 2.0; 95% confidence interval (95% CI) 1.1-3.9], compared with acquiring infection through heterosexual relations and being under 30 years of age (OR 5.9; 95% CI 1.9-17.4), compared with being over 50 years of age. Conclusion: The highest percentage of recent infection was identified in MSM, suggesting either a higher incidence or a greater frequency of HIV testing. Information regarding testing patterns is necessary to correctly interpret data from recently infected individuals. Systems to monitor the HIV epidemic should include both parameters.

Background: Current treatment of chronic hepatitis C virus (HCV) infection has limited efficacy -especially among genotype 1 infected patients-, is costly, and involves severe side effects. Thus, predicting non-response is of major interest for both patient wellbeing and health care expense. At present, treatment cannot be individualized on the basis of any baseline predictor of response. We aimed to identify pre-treatment clinical and virological parameters associated with treatment failure, as well as to assess whether therapy outcome could be predicted at baseline. Methodology: Forty-three HCV subtype 1b (HCV-1b) chronically infected patients treated with pegylated-interferon alpha plus ribavirin were retrospectively studied (21 responders and 22 non-responders). Host (gender, age, weight, transaminase levels, fibrosis stage, and source of infection) and viral-related factors (viral load, and genetic variability in the E1-E2 and Core regions) were assessed. Logistic regression and discriminant analyses were used to develop predictive models. A "leave-one-out" cross-validation method was used to assess the reliability of the discriminant models. Principal Findings: Lower alanine transaminase levels (ALT, p = 0.009), a higher number of quasispecies variants in the E1-E2 region (number of haplotypes, nHap_E1-E2) (p = 0.003), and the absence of both amino acid arginine at position 70 and leucine at position 91 in the Core region (p = 0.039) were significantly associated with treatment failure. Therapy outcome was most accurately predicted by discriminant analysis (90.5% sensitivity and 95.5% specificity, 85.7% sensitivity and 81.8% specificity after cross-validation); the most significant variables included in the predictive model were the Core amino acid pattern, the nHap_E1-E2, and gamma-glutamyl transferase and ALT levels. Conclusions and Significance: Discriminant analysis has been shown as a useful tool to predict treatment outcome using baseline HCV genetic variability and host characteristics. The discriminant models obtained in this study led to accurate predictions in our population of Spanish HCV-1b treatment naive patients.

Background: Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences ( or at least the full coding region) are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. Results: We present and analyse the first complete genome sequence of a HCV subtype Ig isolate. Phylogenetic and genetic distance analyses reveal that HCV-Ig is the most divergent subtype among the HCV-I confirmed subtypes. Potential genomic recombination events between genotypes or subtype I genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-Ig with respect to our sequence. Conclusion: In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.