Epidemiological Surveillance Studies Research Articles

Specific detection of duck adeno-associated virus using a TaqMan-based real-time PCR assay

Duck adeno-associated Virus (DAAV) is a novel pathogen that was recently discovered in ducks. To establish a molecular detection assay for DAAV for further epidemiological investigation and pathogenic mechanism. Here, we designed specific primers and probes according to the sequence characteristics of the newly discovered DAAV and then established a TaqMan real-time PCR method (TaqMan-qPCR) for the detection of DAAV. Our data showed that the established TaqMan-qPCR for detecting DAAV had high sensitivity, with the lowest detection limit of 29.1 copies/μL. No cross reaction was found with duck circovirus (DuCV), H9N2 subtype avian influenza virus (AIV), avian Tembusu virus (ATmV). duck hepatitis A virus 1 and 3 (DHAV-1 and DHAV-3), duck adenovirus A (DAdV-A), duck adenovirus 3 (DAdV-3), or duck enteritis virus (DEV). The repeatability was excellent, with the coefficients of variation of repeated intragroup and intergroup tests ranging from 0.12–0.21% and 0.62–1.42%, respectively. Seventy-eight clinical samples collected from diseased or deceased ducklings were tested. The results showed that the DAAV positive rate was 21.79%, and a triple infection (DAAV+MDPV+GPV) was found. These data provide technical support for further molecular epidemiological surveillance and pathogenic mechanism studies of DAAV infection.

An epidemiologic surveillance study based on wastewater and respiratory specimens reveals influenza a virus prevalence and mutations in Taiyuan, China during 2023-2024.

Influenza is a major cause of morbidity and mortality. Influenza A virus (IAV) is one of the most important pathogens causing influenza and often causes global pandemics due to its tendency to mutate. We aim to use epidemiology based on wastewater and respiratory specimens to understand the occurrence of influenza A virus infections in Taiyuan City. A retrospective epidemiology surveillance was carried out at the First Hospital of Shanxi Medical University (FHSMU) and five wastewater treatment plants (WTPs) in Taiyuan city from 2023 to 2024. Reverse transcription real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) was used to detect influenza A viruses in wastewater and respiratory specimens. High-throughput whole genome sequencing was performed on 17 strains obtained in this study, and subsequent analyses included characterization, phylogenetic construction, amino acid mutation analysis, and antigenic structural variability assessment. 520 wastewater samples and 1,203 throat swab samples were collected. We detected RNA concentration from pH1N1 and H3N2 viruses in wastewater and got 17 genome sequences (5 of pH1N1 and 12 of H3N2) in respiratory specimens. Whole-genome sequencing showed co-prevalence of pH1N1 viruses in the branches of 6B.1A.5a.2a.1 and H3N2 viruses in the branches of 3C.2a1b.2a.2a.3a.a in Taiyuan from 2023 to 2024. Moreover, a HA mutation (N138D), predicted to be of high phenotypic consequence, was found in 8 Taiyuan H3N2 sequences. This study highlights the predominant presence of pH1N1 and H3N2 strains in Taiyuan. The analysis also identified amino acid site variations in the HA antigenic epitopes in H3N2 strains, which may contribute to immune escape.

Development of a LAMP assay for the rapid visual detection of the emerging tick-borne Songling virus

BackgroundSongling virus (SGLV) within the genus Orthonairovirus, family Nairoviridae, is an emerging tick-borne virus associated with human febrile illness. However, no rapid detection method for SGLV has been established.MethodsIn this study, four primer sets targeting the nucleocapsid protein gene of SGLV were designed for use in the LAMP assay and evaluated to identify the optimal primer set. Recombinant plasmids were constructed and utilized for assessing the sensitivity of the assay. Tacheng tick virus 1 (TcTV-1)-, Beiji nairovirus (BJNV)-, Yezo virus (YEZV)-, severe fever with thrombocytopenia syndrome virus (SFTSV)-, and tick-borne encephalitis virus (TBEV)-positive tick samples were utilized to assess the specificity. Field-collected ticks were also evaluated as biological specimens to validate the assay.ResultsA SGLV-specific LAMP assay was established with a detection limit of 1 × 10–2 copies/μl and could be visually confirmed by a color change from purple to blue in SGLV-positive samples. No cross-reactivity was observed in the detection of TcTV-1, BJNV, YEZV, SFTSV, and TBEV using the LAMP assay. In addition to the detection of the same seven high-copy numbers of SGLV as the SYBR Green quantitative RT-PCR assay within a reduced timeframe, the developed LAMP method also effectively identified an additional sample with a low copy number in the field-collected tick samples.ConclusionsWe successfully developed a sensitive, specific, and cost-effective visual method for the rapid detection of SGLV using the LAMP assay, which can be applied in pathogenesis and epidemiological surveillance studies of SGLV.Graphical

Unexpected arboviruses found in an epidemiological surveillance of acute tropical febrile syndrome in the department of Meta, Eastern Colombia

BackgroundNonspecific acute tropical febrile illnesses (NEATFI) are common in the Latin American tropics. Dengue, Chikungunya, Zika, Mayaro, and Usutu, among others, can coexist in the American tropics. This study aimed to surveil the arboviruses that cause| acute febrile syndrome in patients in the Meta department, Colombia. MethodsBetween June 2021 and February 2023, an epidemiological surveillance study was conducted in the Llanos of the Meta department in Eastern Colombia. ResultsOne hundred patients in the acute phase with typical prodromal symptoms of NEATFI infection who attended the emergency department of the Villavicencio Departmental Hospital were included. ELISA tests were performed for Dengue, Usutu, Chikungunya, and Mayaro. RT-qPCR was performed to detect the arboviruses Usutu, Dengue, Zika, Mayaro, and Oropouche. The seroprevalence for the Chikungunya, Mayaro, and Usutu viruses was 41 % (28/68), 40 % (27/67), and 62 % (47/75), respectively. Seroconversion for Chikungunya was observed in one patient; two seroconverted to Mayaro and one to Usutu. The NS5 gene fragment of the Usutu virus was detected in nine febrile patients. RT-qPCR of the remaining arboviruses was negative. The clinical symptoms of the nine Usutu-positive patients were very similar to those of Dengue, Chikungunya, Zika, and Mayaro infections. ConclusionsThe pervasive detection of unexpected viruses such as Usutu and Mayaro demonstrated the importance of searching for other viruses different from Dengue. Because Usutu infection and Mayaro fever have clinical features like Dengue, a new algorithm should be proposed to improve the accuracy of acute tropical fevers.

Comparative antibiotic resistance in urine cultures before and after the SARS-CoV-2 Pandemic

An epidemiological surveillance study was conducted at Laboratorios Ruiz (member of Synlab México group) in Puebla, Mexico that included the comparison of the antibiotic susceptibility test results of bacteria isolated from urine cultures at two different periods, between 2017 and 2021. There was an increase in the resistance to beta-lactams in E. coli and K. pneumoniae while a decrease in resistance to aminoglycosides in E. faecalis. The COVID-19 pandemic may have contributed to the increased antibiotic resistance trends.

Microorganisms isolated from blood cultures and resistance profile in children with cancer and high-risk febrile neutropenia. Red PINDA, Chile, 2016-2021

To identify the frequency of microorganisms isolated from blood cultures (BC) and their antimicrobial resistance (R) profile in children with HRFN, compared with the same data from previous studies of the same group. Prospective, multicenter, epidemiological surveillance study of microorganisms isolated from BC in patients under 18 years of age, from 7 PINDA network hospitals, between 2016 and 2021. 284 episodes of HRFN with positive BC were analyzed out of 1091 enrolled episodes (26%). Median age 7.2 years [3.0-12.3]. The main isolates were gram-negative bacilli (GNB) 49.2%, gram-positive cocci (GPC) 43.8%, and fungi 3.6%. The most frequently isolated microorganisms were viridans group Streptococci (VGS) (25.8%), Escherichia coli (19.8%), Pseudomonas spp. (11.2%), Klebsiella spp. (10.9%), and coagulase negative Staphylococci (CoNS) (10.9%). There was an increase in R to third-generation cephalosporins (p = 0.011) in GNB and to oxacillin in CoNS (p = 0.00), as well as a decrease in R to amikacin in non-fermenting GNB (p = 0.02) and to penicillin in VGS (p = 0.04). VGS is the main agent isolated in BC from pediatric patients with cancer and episodes of HRFN, followed by E. coli, Pseudomonas spp., and Klebsiella spp. Having epidemiological surveillance of microorganisms isolated from BC and their antimicrobial R profile is essential to favor the rational use of antimicrobials.

KPC-2 allelic variants in Klebsiella pneumoniae isolates resistant to ceftazidime-avibactam from Argentina: blaKPC-80, blaKPC-81, blaKPC-96 and blaKPC-97.

The emergence of ceftazidime-avibactam (CZA) resistance poses a significant threat to the efficacy of this life-saving therapy against carbapenem-resistant bacteria, particularly Klebsiella pneumoniae-producing KPC enzymes. This study investigates four clinical isolates exhibiting resistance to CZA, revealing novel allelic variants of the key resistance gene, blaKPC-2. The mutations identified in hotspots surrounding the active site of KPC, such as K269_D270insPNK, del_I173, Y241N and V277_I278insNSEAV, prove the adaptability of these pathogens. Intriguingly, low-level resistance to imipenem and disruptions in porin genes were observed, emphasizing the complexity of the resistance mechanisms. Interestingly, three of four isolates belonged to clonal complex 11. This research not only sheds light on the clinical significance of CZA resistance but also shows the urgency for comprehensive surveillance and molecular studies to inform effective antimicrobial treatment strategies in the face of evolving bacterial resistance.

An epidemiological surveillance study (2021–2022): detection of a high diversity of Clostridioides difficile isolates in one tertiary hospital in Chongqing, Southwest China

BackgroundClostridioides difficile is a bacterium that causes antibiotic-associated infectious diarrhea and pseudomembranous enterocolitis. The impact of C. difficile infection (CDI) in China has gained significant attention in recent years. However, little epidemiological data are available from Chongqing, a city located in Southwest China. This study aimed to investigate the epidemiological pattern of CDI and explore the drug resistance of C. difficile isolates in Chongqing.MethodsA case-control study was conducted to investigate the clinical infection characteristics and susceptibility factors of C. difficile. The features of the C. difficile isolates were evaluated by testing for toxin genes and using multi-locus sequence typing (MLST). The susceptibility of strains to nine antibiotics was determined using agar dilution technique.ResultsOut of 2084 diarrhea patients, 90 were tested positive for the isolation of toxigenic C. difficile strains, resulting in a CDI prevalence rate of 4.32%. Tetracycline, cephalosporins, hepatobiliary disease, and gastrointestinal disorders were identified as independent risk factors for CDI incidence. The 90 strains were classified into 21 sequence types (ST), with ST3 being the most frequent (n = 25, 27.78%), followed by ST2 (n = 10, 11.11%) and ST37 (n = 9, 10%). Three different toxin types were identified: 69 (76.67%) were A+B+CDT−, 12 (13.33%) were A−B+CDT−, and 9 (10%) were A+B+CDT+. Although substantial resistance to erythromycin (73.33%), moxifloxacin (62.22%), and clindamycin (82.22%), none of the isolates exhibited resistance to vancomycin, tigecycline, or metronidazole. Furthermore, different toxin types displayed varying anti-microbial characteristics.ConclusionsThe strains identified in Chongqing, Southwest China, exhibited high genetic diversity. Enhance full awareness of high-risk patients with HA-CDI infection, particularly those with gastrointestinal and hepatocellular diseases, and emphasize caution in the use of tetracycline and capecitabine. These findings suggest that a potential epidemic of CDI may occur in the future, emphasizing the need for timely monitoring.

Decreasing alcohol use among young adults presenting for service in the U.S. Air Force: An epidemiological surveillance study

ABSTRACT U.S. surveys demonstrate recent decreases in the prevalence of alcohol use and binge drinking among young adults. The current study aims to determine whether similar trends are evident in a similarly aged cohort of service members in the US Air Force to inform ongoing prevention efforts. Participants were 103,240 Air Force personnel in entry-level training between 2016 and 2019. Participants anonymously completed the AUDIT (Alcohol Use Disorder Identification Test) regarding their pre-service drinking. Logistic regression analyses and the Cochran-Armitage test were conducted to measure population trends over the study duration with stratification by age (<21 vs. ≥21) and evaluation of specific alcohol behaviors. Between 2016 and 2019, the proportion of young service members endorsing any alcohol use significantly decreased for both the <21 group (i.e. from 38.9% to 32.6%) and the ≥21 group (i.e. from 80.6% to 77.5%). Among those who endorsed drinking, a decrease over time in binge use was also observed from 46.6% to 37.8% for the <21 group and from 34.2% to 27.5% for the ≥21 group. Responses to other specific alcohol risk items and total AUDIT scores also demonstrated decreases. Binge use and risky drinking remained disproportionately common among those under the legal drinking age. It is encouraging to observe a shift toward abstinence and decreased binge use among this population of young military recruits. However, given the risk for many adverse health and legal consequences in this population, more work is needed to prevent problematic drinking, especially among those under the legal drinking age.

Jingmen tick virus: an emerging arbovirus with a global threat.

Jingmen tick virus (JMTV), belonging to the Flaviviridae family, is a novel segmented RNA virus identified in 2014 in the Jingmen region of Hubei Province, China. Up to now, JMTV has been detected in a variety of countries or regions in Asia, Europe, Africa, and the Americas, involving a wide range of arthropods and mammals, and even humans. The JMTV genome is composed of four linear RNA segments, two of which are derived from flaviviruses, while the other two segments are unique to JMTV and has no matching virus. Currently, JMTV has been shown to have a pathogenic effect on humans. Humans who had been infected would develop viremia and variable degrees of clinical symptoms. However, the pathogenic mechanism of JMTV has not been elucidated yet. Therefore, it is crucial to strengthen the epidemiological surveillance and laboratory studies of JMTV.

Genome analyses ofspecies A rotavirus isolated from various mammalian hosts inNorthern Ireland during 2013-2016.

Rotavirus group A (RVA) is the most important cause of acute diarrhoea and severe dehydration in young mammals. Infection in livestock is associated with significant mortality and economic losses and, together with wildlife reservoirs, acts as a potential source of zoonotic transmission. Therefore, molecular surveillance of circulating RVA strains in animal species is necessary to assess the risks posed to humans and their livestock. An RVA molecular epidemiological surveillance study on clinically diseased livestock species revealed high prevalence in cattle and pigs (31 per cent and 18 per cent, respectively) with significant phylogenetic diversity including a novel and divergent ovine artiodactyl DS-1-like constellation G10-P[15]-I2-R2-C2-M2-A11-N2-T6-E2-H3. An RVA gene reassortment occurred in an RVA asymptomatic pig and identified as a G5-P[13] strain, and a non-structural protein (NSP)2 gene had intergenomically reassorted with a human RVA strain (reverse zoonosis) and possessed a novel NSP4 enterotoxin E9 which may relate to the asymptomatic RVA infection. Analysis of a novel sheep G10-P[15] strain viral protein 4 gene imparts a putative homologous intergenic and interspecies recombination event, subsequently creating the new P[15] divergent lineage. While surveillance across a wider range of wildlife and exotic species identified generally negative or low prevalence, a novel RVA interspecies transmission in a non-indigenous pudu deer (zoo origin) with the constellation of G6-P[11]12-R2-C2-M2-A3-N2-T6-E2-H3 was detected at a viral load of 11.1 log10 copies/gram. The detection of novel emerging strains, interspecies reassortment, interspecies infection, and recombination of RVA circulating in animal livestock and wildlife reservoirs is of paramount importance to the RVA epidemiology and evolution for the One Health approach and post-human vaccine introduction era where highly virulent animal RVA genotypes have the potential to be zoonotically transmitted.

Legionellosis-Associated Hospitalization in Spain from 2002 to 2021.

Legionellosis is a respiratory disease of bacterial and environmental origin that usually presents two distinct clinical entities, "Legionnaires' disease" (LD) and "Pontiac fever". LD is an important cause of hospital-acquired pneumonia (HAP). The objective of this study is to describe the epidemiology of legionellosis-associated hospitalization (L-AH) in Spain from 2002 to 2021 and the burden of hospitalization due to legionellosis. Discharge reports from the Minimum Basic Data Set (MBDS) were used to retrospectively analyze hospital discharge data with a diagnosis of legionellosis, based on the ICD-9-CM and ICD-10-CM diagnosis codes, from 2002 to 2021. 21,300 L-AH occurred throughout the year during 2002-2021. The incidence of hospitalization associated per 100,000 inhabitants by month showed a similar trend for the 2002-2011, 2012-2021, and 2002-2021 periods. In Spain, during 2002-2021, the hospitalization rate (HR) in the autonomous communities ranged from 4.57 (2002-2011) to 0.24 (2012-2021) cases per 100,000 inhabitants. The HR of legionellosis in Spain has substantially increased across the 2002-2021 period, and the estimate is consistent with available European data. It is considered that in-depth epidemiological surveillance studies of legionellosis and improvements in the prevention and control of the disease are required in Spain.

男子大学生ラグビー選手の外傷・障害特性

The purpose of this study was to describe the incidence, severity, and burden of injuries in Japanese male collegiate rugby union players. Initially, 170 male collegiate rugby union players from one university club were registered in this epidemiological surveillance study. The occurrence of injuries was recorded by a team medical staff during the 2017–2021 playing seasons. The incidence of injuries was 6.87 injuries/1000 h. This incidence was significantly higher during matches (100.37 injuries/1000 h) than that during training (3.63 injuries/1000 h). The severity of injuries was 31.0 days, and there were no significant differences between matches and training, or forwards and backs. The burden of injuries was 213.1 days/1000 h. This burden was significantly higher during matches (2887.8 days/1000 h) compared to training (120.1 days/1000 h). Matches had higher incidence of ankle sprain/ligament injuries (15.80 injuries/1000 h) and concussion (15.36 injuries/1000 h). The most common injury site was the ankle (1.24 injuries/1000 h). However, the greatest severity and burden were observed for knee injuries (severity: 59.1 days, burden: 48.6 days/1000 h). Furthermore, the greatest burden of injury type was knee sprain/ligament injuries (39.4 days/1000 h). In addition, the incidence of acromioclavicular joint injury was significantly higher in forwards, whereas hamstring strain was significantly higher in backs. The common injury mechanisms identified were being tackled (16.0%) and tackling (14.7%), followed by overuse (12.1%). In order to improve the player welfare of the Japanese collegiate rugby union players, it is necessary to work on the prevention strategy considering the injury profile.

Emergence and evolution of drug-resistant Mycobacterium tuberculosis in eastern China: A six-year prospective study

Understanding the emergence and evolution of drug resistance can inform public health intervention to combat tuberculosis (TB). In this prospective molecular epidemiological surveillance study from 2015 to 2021 in eastern China, we prospectively collected whole-genome sequencing and epidemiological data on TB patients. We dissect the ordering of drug resistance mutation acquisition for nine commonly used anti-TB drugs, and we found that the katG S315T mutation first appeared around 1959, followed by rpoB S450L (1969), rpsL L43A (1972), embB M306V (1978), rrs 1401 (1981), fabG1 (1982), pncA (1985) and folC (1988) mutations. GyrA gene mutations appeared after the year of 2000. We observed that the first expansion of Mycobacterium tuberculosis (M.tb) resistance population among eastern China appeared after the introduction of isoniazid, streptomycin and para-amino salicylic acid, and the second expansion after the ethambutol, rifampicin, pyrazinamide, ethionamide and aminoglycosides. We speculate these two expansions are linked with population shift historically. By geospatial analysis, we found drug-resistant isolates migrated within eastern China. With epidemiological data of clonal strains, we observed some strains can evolve continuously in individuals and transmit readily in a population. In conclusion, this study mirrored the emergence and evolution of drug-resistant M.tb in eastern China were linked to the sequence and timing of introduction of anti-TB drugs, and multiple factors may contribute to the resistant population enlarged. To resolve the epidemic of drug-resistant TB, it requires applying anti-TB drugs carefully and/or identifying resistant patients timely to prevent them from developing high-level resistance and transmitting to others.

A multiplex PCR assay for the differentiation of Mycobacterium tuberculosis complex reveals high rates of mixed-lineage tuberculosis infections among patients in Ghana.

In low-resource settings with high tuberculosis (TB) burdens, lack of rapid diagnostic methods for detection and differentiation of Mycobacterium tuberculosis complex (MTBC) is a major challenge affecting TB management. This study utilized comparative genomic analyses of MTBC lineages; M. tuberculosis, M. africanum Lineages 5/6 and M. bovis to identify lineage-specific genes. Primers were designed for the development of a Multiplex PCR assay which was successful in differentiating the MTBC lineages. There was no cross-reaction with other respiratory pathogens tested. Validation of the assay using clinical samples was performed with sputum DNA extracts from 341 clinically confirmed active TB patients. It was observed that 24.9% of cases were caused by M. tuberculosis, while M. africanum L5 & L6 reported 9.0% and 14.4%, respectively. M. bovis infection was the least frequently detected lineage with 1.8%. Also, 27.0% and 17.0% of the cases were PCR negative and unspeciated, respectively. However, mixed-lineage TB infections were recorded at a surprising 5.9%. This multiplex PCR assay will allow speciation of MTBC lineages in low-resource regions, providing rapid differentiation of TB infections to select appropriate medication at the earliest possible time point. It will also be useful in epidemiological surveillance studies providing reliable information on the prevalence of TB lineages as well as identifying difficult to treat cases of mixed-lineage tuberculosis infections.

The Effect of Decreased Antipseudomonal Drug Consumption on Pseudomonas aeruginosa Incidence and Antimicrobial Susceptibility Profiles over 9 Years in a Lebanese Tertiary Care Center

Pseudomonas aeruginosa (PAE) is intrinsically resistant to numerous classes of antimicrobials such as tetracycline and β-lactam antibiotics. More epidemiological surveillance studies on the antimicrobial susceptibility profiles of PAE are needed to generate clinically significant data and better guided therapeutic options. We describe and analyze in a retrospective study the epidemiologic trends of 1827 Pseudomonas spp. isolates (83.5% PAE, 16.4% Pseudomonas sp., and 0.2% Pseudomonas putida) from various clinical specimens with their resistance patterns to antimicrobial consumption at a tertiary medical center in Lebanon between January 2010 and December 2018. We report a significant drop in the incidence of PAE from sputum (p-value = 0.05), whereas bloodstream infection isolation density showed no trend over the study period. We also registered a minimal but statistically significant drop in resistance of Pseudomonas to certain antibiotics and a decrease in the consumption of antipseudomonal antibiotics (p-value < 0.001). Only 61 PAE isolates from a total of 1827 Pseudomonas cultures (3.33%) were difficult to treat, of which only one was a bacteremia. Interestingly, we found that the carbapenem susceptibility of Pseudomonas was unaffected by the decrease in their consumption. These results augur that antimicrobial pressure may not be the sole contributor to resistance emergence. Finally, antimicrobial stewardship seems to have a positive impact on nosocomial epidemiology.

Monitoring the Establishment of VOC Gamma in Minas Gerais, Brazil: A Retrospective Epidemiological and Genomic Surveillance Study.

Since its first identification in Brazil, the variant of concern (VOC) Gamma has been associated with increased infection and transmission rates, hospitalizations, and deaths. Minas Gerais (MG), the second-largest populated Brazilian state with more than 20 million inhabitants, observed a peak of cases and deaths in March-April 2021. We conducted a surveillance study in 1240 COVID-19-positive samples from 305 municipalities distributed across MG's 28 Regional Health Units (RHU) between 1 March to 27 April 2021. The most common variant was the VOC Gamma (71.2%), followed by the variant of interest (VOI) zeta (12.4%) and VOC alpha (9.6%). Although the predominance of Gamma was found in most of the RHUs, clusters of Zeta and Alpha variants were observed. One Alpha-clustered RHU has a history of high human mobility from countries with Alpha predominance. Other less frequent lineages, such as P.4, P.5, and P.7, were also identified. With our genomic characterization approach, we estimated the introduction of Gamma on 7 January 2021, at RHU Belo Horizonte. Differences in mortality between the Zeta, Gamma and Alpha variants were not observed. We reinforce the importance of vaccination programs to prevent severe cases and deaths during transmission peaks.

Risk factors for SARS-CoV-2 transmission in close contacts of adults at high risk of infection due to occupation: results from the contact tracing strategy of the CoVIDA epidemiological surveillance study in Bogotá, Colombia, in 2020–2021

ObjectivesTo estimate the risk factors for SARS-CoV-2 transmission in close contacts of adults at high risk of infection due to occupation, participants of the CoVIDA study, in Bogotá D.C., Colombia.SettingThe...

Culture-Independent Detection and Identification of Leptospira Serovars.

Pathogenic Leptospira, the causative agents of leptospirosis, comprise >200 serotypes (called serovars). Most have a restricted reservoir-host range, and some, e.g., serovar Copenhageni, are cosmopolitan and of public health importance owing to their propensity to produce severe, fatal disease in humans. Available serotyping approaches-such as multilocus sequence typing, core genome sequence typing, pulsed-field gel electrophoresis, and the cross-agglutination absorption test-are tedious and expensive, and require isolation of the organisms in culture media-a protracted and incredibly inefficient process-precluding their use in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. Here, we have developed a simple yet specific real-time qPCR assay-targeting a Leptospira-unique gene encoding a putative polysaccharide flippase-that provides intraspecies, serotype-defining (i.e., epidemiologically useful) information, and improves upon the sensitivity of preferred lipL32-based qPCR-based diagnostic tests. The assay, dubbed RAgI ("rage one"), is rapid and affordable, and reliably and specifically detects group I pathogenic Leptospira in culture, serum, and urine, with no detectable off-target amplification-even of the genetically related but low virulence group II pathogenic (formerly "intermediate") or nonpathogenic Leptospira. It retained 100% diagnostic specificity when tested against difficult sample types, including field-collected dog urine samples and environmental samples containing varied and complex microbial species-consortia. This assay holds considerable promise in the clinical setting, and for routine epidemiological and environmental surveillance studies. IMPORTANCE Leptospirosis is caused by a diverse group of pathogenic spirochetes comprising over 200 different serotypes. Some are widely reported and of public health importance owing to their propensity to produce severe, fatal disease in humans. Apart from their tedium and expense, current serotyping approaches require isolation of the organisms in culture media-a protracted and incredibly inefficient process-rendering them useless clinically and limiting their utilization in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. The 11108 qPCR-assay overcomes this barrier to progress via direct taxonomic and serotype classification of Leptospira from urine and serum samples, and hence, is the first qPCR-based prognostic test for human leptospirosis.

Opioid-related adverse drug reactions in patients visiting the emergency division of a tertiary hospital.

Opioid use and associated morbidity and mortality have increased in several countries during the past 20 years. We performed a study whose objective was to assess the frequency and causes of opioid-related emergency division (ED) visits in an adult tertiary Swiss University Hospital over 9 weeks in 2018. We primarily assessed opioid-related adverse drug reactions (ADR), secondary overdose, misuse, abuse, and insufficient pain relief. Current opioid use was identified in 1037 (8.3%) of the 12 470 included ED visits. In 64 opioid users, an ADR was identified as a contributing cause of the ED visit, representing 6.2% of opioid users, and 0.5% of the total ED visits. Moreover, we identified an overdose in 16 opioid users, misuse or abuse in 19 opioid users, and compatible withdrawal symptoms in 7 opioid users. After pooling all these events, we conclude that the ED visits could be related to opioid use in 10.2% of opioid users. Finally, in 201 opioid users, insufficient pain relief (pain not responding to the current pharmacological treatment) was identified as a contributing cause of ED visits. In these cases, other factors than simply pharmacological nonresponse may have been involved. In the context of an ever-increasing opioid use to better control chronic pain situations, these results should reinforce emergency network epidemiological surveillance studies at a national level.