Performance of SARS-CoV-2 nucleic acid amplification testing in Austria as measured by external quality assessment schemes during 3 years of the COVID-19 pandemic: an observational retrospective study.

BACKGROUND: The aim of external quality assessment (EQA) schemes is to evaluate the analytical performance of laboratories and test systems in a near-to-real-life setting. This monitoring service provides feedback to participant laboratories and serves as a control measure for the epidemiological assessment of the regional incidence of a pathogen, particularly during epidemics. Using data from EQA schemes implemented as a result of the intensive effort to monitor SARS-CoV-2 infections in Austria, we aimed to identify factors that explained the variation in laboratory performance for SARS-CoV-2 detection over the course of the COVID-19 pandemic. METHODS: For this observational study, we retrospectively analysed 6308 reverse transcriptase quantitative PCR (RT-qPCR) test results reported by 191 laboratories on 71 samples during 14 rounds of three SARS-CoV-2 pathogen detection EQA schemes in Austria between May 18, 2020, and Feb 20, 2023. We calculated the overall rates of false and true-negative, false and true-positive, and inconclusive results. We then assessed laboratory performance by estimating the sensitivity by testing whether significant variation in the odds of obtaining a true-positive result could be explained by virus concentration, laboratory type, or assay format. We also assessed whether laboratory performance changed over time. FINDINGS: 4371 (93·7%) of 4663 qPCR test results were true-positive, 241 (5·2%) were false-negative, and 51 (1·1%) were inconclusive. The mean per-sample sensitivity was 99·7% in samples with high virus concentrations (1383 [99·4%] true-positive, three [0·2%] false-negative, and five [0·4%] inconclusive results for 1391 tests in which the sample cycle threshold was ≤32), whereas detection rates were lower in samples with low virus concentrations (mean per-sample sensitivity 92·5%; 2988 [91·3%] true-positive, 238 [7·3%] false-negative, and 46 [1·4%] inconclusive results for 3272 tests in which the cycle threshold was >32). Of the 1645 results expected to be negative, 1561 (94·9%) were correctly reported as negative, 10 (0·6%) were incorrectly reported as positive, and 74 (4·5%) were reported as inconclusive. Notably, the overall performance of the tests did not change significantly over time. The odds of reporting a correct result were 2·94 (95% CI 1·75-4·96) times higher for a medical laboratory than for a non-medical laboratory, and 4·60 (2·91-7·41) times greater for automated test systems than for manual test systems. Automated test systems within medical laboratories had the highest sensitivity when compared with systems requiring manual intervention in both medical and non-medical laboratories. INTERPRETATION: High rates of false-negativity in all PCR analyses evaluated in comprehensive, multiple, and repeated EQA schemes outline a clear path for improvement in the future. The performance of some laboratories (eg, non-medical laboratories or those using non-automated test systems) should receive additional scrutiny-for example, by requiring additional EQA schemes for certification or accreditation-if the aggregated data from EQA rounds suggest lower sensitivity than that recorded by others. This strategy will provide assurances that epidemiological data as a whole are reliable when testing on such a large scale. Although performance did not improve over time, we cannot exclude extenuating circumstances-such as shortages and weakened supply chains-that could have prevented laboratories from seeking alternative methods to improve performance. FUNDING: None.

Genetic characterization of Escherichia coli and Klebsiella spp. from humans and poultry in Nigeria.

The emergence of antibiotic resistance in livestock, especially food-producing animals, is of major public health importance as a result of the possibility of these bacteria entering the food chain. In this study, the genetic characteristics of antibiotic-resistant Escherichia coli and Klebsiella spp. isolates from humans and poultry in Edo state, Nigeria, were investigated. In April 2017, 45 Klebsiella spp. and 46 E. coli isolates were obtained from urine, clinical wounds, nasal and chicken faecal samples. Isolates were recovered and identified as previously described. Species identification was achieved by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing. Antimicrobial susceptibility testing was carried out using the Kirby-Bauer method for 12 antibiotics. A double disc synergy test was used to screen for extended-spectrum beta-lactamse (ESBL) production. Whole genome sequencing was performed for strain characterization of the isolates. Thirteen Klebsiella spp. isolates yielded positive results by the ESBL phenotypic test and harboured ESBL genes. Of the 46 E. coli isolates, 21 human and 13 poultry isolates were resistant to at least one of the tested antibiotics. Four human E. coli isolates harboured ESBL genes and revealed positive results when applying ESBL double disc synergy tests. ESBL genes in the Klebsiella spp. and E. coli isolates include bla CTX-M-15 and bla SHV-28. Whole genome-based core gene multilocus sequence typing of the Klebsiella spp. and E. coli isolates revealed a close relatedness among the isolates. An integrated 'One Health' surveillance system is required to monitor transmission of antimicrobial resistance in Nigeria.

Design of external quality assessment schemes and definition of the roles of their providers in future epidemics.

During an epidemic, individual test results form the basis of epidemiological indicators such as case numbers or incidence. Therefore, the accuracy of measures derived from these indicators depends on the reliability of individual results. In the COVID-19 pandemic, monitoring and evaluating the performance of the unprecedented number of testing facilities in operation, and novel testing systems in use, was urgently needed. External quality assessment (EQA) schemes are unique sources of data reporting on testing performance, and their providers are recognised contacts and support for test facilities (for technical-analytical topics) and health authorities (for planning the monitoring of infection diagnostics). To identify information provided by SARS-CoV-2 genome detection EQA schemes that is relevant for public health microbiology, we reviewed the current literature published in PubMed between January, 2020, and July, 2022. We derived recommendations for EQA providers and their schemes for best practices to monitor pathogen-detection performance in future epidemics. We also showed laboratories, test facilities, and health authorities the information and benefits they can derive from EQA data, and from the non-EQA services of their providers.

Ultra-rapid rollout vaccination with BNT162b2 to reduce SARS-CoV-2 infections in the general population.

This study aimed to determine the impact of ultra-rapid rollout vaccination on incidence of SARS-CoV-2 infection. Vaccination with BNT162b2 was provided to 66.9% of eligible residents of the Schwaz district in Tyrol, Austria, within six days per dose (first dose: 11-16 March 2021, second dose: 8-13 April 2021). Of 11,955 individuals enrolled at nine vaccination centers (median age 44.6 years; 51.3% female), 71 had incident SARS-CoV-2 over a six-month follow-up. Incidence rates per 100,000 person-weeks were 92.3 (95% confidence interval [CI]: 70.8-120.2) at weeks 1-5 and 6.4 (3.9-10.4) at ≥6 weeks after dose 1. In these two periods, effectiveness of the vaccination campaign to reduce incident SARS-CoV-2 was 58.6% (50.8%-65.2%) and 91.1% (89.6%-92.3%) in study participants and 28.3% (23.1%-33.0%) and 64.0% (61.7%-66.1%) in the Schwaz district, compared with districts with slower vaccination rollout. Therefore, the vaccination campaign in the Schwaz district illustrates the impact of accelerated vaccination rollout in controlling the pandemic.

Characterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria.

Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49 E. coli, 27 E. faecalis, 7 K. pneumoniae and 6 E. faecium. Clusters of isolates from the same species obtained in different sample collection dates were detected. Of the isolates, 29.2% were resistant to at least one antimicrobial. E. coli and E. faecalis isolates from different compartments had acquired antimicrobial resistance genes (ARGs) associated with veterinary drugs such as aminoglycosides and tetracyclines, some of which were carried in conjugative and mobilizable plasmids. Three multidrug resistant (MDR) E. coli isolates were found in samples from field drainage and wastewater. Early detection of ARGs and ARB in natural and farm-related environments can identify hotspots of AMR and help prevent its emergence and dissemination along the food/feed chain.

Draft Genome Sequence of Citrobacter cronae Awk (Sequence Type 880), Associated with Edible Snails Commercially Available in Awka, Nigeria.

We describe the draft genome sequence and annotation of Citrobacter cronae strain Awk (sequence type 880), recovered from fresh edible snails (Achatina achatina) commercially available in Awka Metropolis, Nigeria. The genome contains 4,629 protein-coding genes, 107 RNA-coding genes, and several antimicrobial resistance genes, including blaCMY-98 and qnrB12.

Viral variant-resolved wastewater surveillance of SARS-CoV-2 at national scale.

SARS-CoV-2 surveillance by wastewater-based epidemiology is poised to provide a complementary approach to sequencing individual cases. However, robust quantification of variants and de novo detection of emerging variants remains challenging for existing strategies. We deep sequenced 3,413 wastewater samples representing 94 municipal catchments, covering >59% of the population of Austria, from December 2020 to February 2022. Our system of variant quantification in sewage pipeline designed for robustness (termed VaQuERo) enabled us to deduce the spatiotemporal abundance of predefined variants from complex wastewater samples. These results were validated against epidemiological records of >311,000 individual cases. Furthermore, we describe elevated viral genetic diversity during the Delta variant period, provide a framework to predict emerging variants and measure the reproductive advantage of variants of concern by calculating variant-specific reproduction numbers from wastewater. Together, this study demonstrates the power of national-scale WBE to support public health and promises particular value for countries without extensive individual monitoring.

Association of Phylogenomic Relatedness among Neisseria gonorrhoeae Strains with Antimicrobial Resistance, Austria, 2016-2020.

We investigated genomic determinants of antimicrobial resistance in 1,318 Neisseria gonorrhoeae strains isolated in Austria during 2016-2020. Sequence type (ST) 9363 and ST11422 isolates had high rates of azithromycin resistance, and ST7363 isolates correlated with cephalosporin resistance. These results underline the benefit of genomic surveillance for antimicrobial resistance monitoring.

Dermatitis linearis outbreak associated with Paederus balcanicus in Austria.

BACKGROUND: Dermatitis linearis is a toxic skin lesion caused by contact with certain beetles of the genus Paederus (Coleoptera: Staphylinidae). Dermatitis linearis outbreaks have been described mainly in tropical and subtropical regions, but so far not in Central Europe, and are considered an emerging public health concern potentially associated with climate change. MATERIAL AND METHODS: Following diagnosis of dermatitis linearis in a cluster of six adults and one child with reported exposure to beetles with morphological characteristics of Paederus species at a recreational public open-air bath at Lake Neusiedl (Illmitz, Burgenland, Austria), we performed on-site inspection and installed light and pitfall traps. Collected beetle specimens of the genus Paederus were classified using morphological characteristics and DNA barcoding. RESULTS: A total of 32 Paederus beetles were collected using an aspirator (n = 2) and light traps (n = 30). No individuals of the genus Paederus were captured with the pitfall traps. Morphological analyses identified them as members of the Paederus balcanicus species, which was confirmed by genetic specification of four arbitrarily chosen individuals. Dermatitis linearis lesions were treated with topical steroids and healed but partly leaving scars and hyperpigmentation, over the course of a few weeks in all affected persons. CONCLUSION: We report for the first time (a) an outbreak of dermatitis linearis associated with exposure to autochthonous Paederus species in Austria, and (b) that contact to the species Paederus balcanicus may cause dermatitis linearis in humans. Adequate measures should be taken to prevent dermatitis linearis outbreaks in areas with resident Paederus occurrence.

Rifampicin Resistance Associated with rpoB Mutations in Neisseria gonorrhoeae Clinical Strains Isolated in Austria, 2016 to 2020.

Due to increasing rates of antimicrobial resistance (AMR) in Neisseria gonorrhoeae, alternative treatments should be considered. To assess rifampicin's potential as a gonorrhea treatment, we used rpoB mutations to estimate rifampicin resistance in Austrian N. gonorrhoeae isolates. We found 30% of resistant isolates clustering in three main phylogenomic branches. Rifampicin resistance was associated with resistance to other antibiotics. Therefore, rifampicin cannot be recommended as an alternative gonorrhea treatment in Austria, even in combination therapy. IMPORTANCE Gonorrhea, caused by Neisseria gonorrhoeae, is one of the most common bacterial sexually transmitted infections. It is treated with antibiotics, but an increasing number of N. gonorrhoeae strains are resistant to currently used treatments. In this study, we explored the potential of rifampicin, another antibiotic, as a treatment option for gonorrhea. However, around 30% of Austrian N. gonorrhoeae strains investigated were already resistant to rifampicin, which would limit its benefit as a gonorrhea treatment.

Genome Sequence of OXA-726-Encoding Aeromonas dhakensis Igbk (Sequence Type 1171) from an Edible Snail Traded in Nigeria.

Aeromonas dhakensis is the most virulent Aeromonas species pathogenic to both animals and humans. The degree of its risk to health seems masked by misidentifications. We present the genome sequence of A. dhakensis Igbk (sequence type 1171), associated with snails, harboring the OXA-726 gene in the chromosome.

Genetic Characterization of Antibiotic Resistant Enterobacteriaceae Isolates From Bovine Animals and the Environment in Nigeria.

There is a link between antibiotic resistance in humans, livestock and the environment. This study was carried out to characterize antibiotic resistant bovine and environmental Enterobacteriaceae isolates from Edo state, Nigeria. A total of 109 consecutive isolates of Enterobacteriaceae were isolated from March-May 2015 from 150 fecal samples of healthy bovine animals from three farms at slaughter in Edo state Nigeria. Similarly, 43 Enterobacteriaceae isolates were also obtained from a total of 100 environmental samples from different sources. Isolates were recovered and identified from samples using standard microbiological techniques. Recovered isolates were pre-identified by the Microbact Gram-Negative identification system and confirmed with Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing (rMLST). Antibiotic susceptibility testing was carried out by Kirby-Bauer method for 14 antibiotics. Whole genome sequencing (WGS) was carried out for isolate characterization and identification of resistance determinants. Out of 109 animal and 43 environmental Enterobacteriaceae isolates, 18 (17%) and 8 (19%) isolates based on selection criteria showed antibiotic resistance and were further investigated by whole genome sequencing (WGS). Resistance genes were detected in all (100%) of the resistant bovine and environmental Enterobacteriaceae isolates. The resistance determinants included ß-lactamase genes, aminoglycoside modifying enzymes, qnr genes, sulfonamide, tetracycline and trimethoprim resistance genes, respectively. Out of the 18 and 8 resistant animal and environmental isolates 3 (17%) and 2 (25%) were multidrug resistant (MDR) and had resistance determinants which included efflux genes, regulatory systems modulating antibiotic efflux and antibiotic target alteration genes. Our study shows the dissemination of antibiotic resistance especially MDR strains among Nigerian bovine and environmental Enterobacteriaceae isolates. The presence of these resistant strains in animals and the environment constitute a serious health concern indicated by the difficult treatment options of the infections caused by these organisms. To the best of our knowledge we report the first detailed genomic characterization of antibiotic resistance in bovine and environmental Enterobacteriaceae isolates for Nigeria.

First Nationwide Monitoring Program for the Detection of Potentially Invasive Mosquito Species in Austria.

In Austria, only fragmented information on the occurrence of alien and potentially invasive mosquito species exists. The aim of this study is a nationwide overview on the situation of those mosquitoes in Austria. Using a nationwide uniform protocol for the first time, mosquito eggs were sampled with ovitraps at 45 locations in Austria at weekly intervals from May to October 2020. The sampled eggs were counted and the species were identified by genetic analysis. The Asian tiger mosquito Aedes albopictus was found at two sites, once in Tyrol, where this species has been reported before, and for the first time in the province of Lower Austria, at a motorway rest stop. The Asian bush mosquito Aedes japonicus was widespread in Austria. It was found in all provinces and was the most abundant species in the ovitraps by far. Aedes japonicus was more abundant in the South than in the North and more eggs were found in habitats with artificial surfaces than in (semi-) natural areas. Further, the number of Ae. japonicus eggs increased with higher ambient temperature and decreased with higher wind speed. The results of this study will contribute to a better estimation of the risk of mosquito-borne disease in Austria and will be a useful baseline for a future documentation of changes in the distribution of those species.

Outbreak of Cronobacter turicensis in European brown hares (Lepus europaeus).

This is the first report of acute deaths in five European brown hares (Lepus europaeus) attributed to mucoid and necrotizing typhlocolitis caused by genetically different Cronobacter (C.) turicensis strains in northeastern Austria. As this opportunistic pathogen is mainly known for causing disease in immunocompromised humans and neonates, this previously unrecognized potential for a spill over from a wildlife reservoir to humans warrants further attention.

Comparison of Automated Ribotyping, spa Typing, and MLST in 108 Clinical Isolates of Staphylococcus aureus from Orthopedic Infections.

108 isolates of Staphylococcus aureus, belonging to six large ribogroups according to the automated Ribo-Printer® system, were studied with two highly used molecular methods for epidemiological studies, namely multi-locus sequence typing (MLST) and spa typing, followed by BURP and eBURST v3 analysis for clustering spa types and sequence (ST) types. The aim was to evaluate whether automated ribotyping could be considered a useful screening tool for identifying S. aureus genetic lineages with respect to spa typing and MLST. Clarifying the relationship of riboprinting with these typing methods and establishing whether ribogroups fit single clonal complexes were two main objectives. Further information on the genetic profile of the isolates was obtained from agr typing and the search for the mecA, tst genes, and the IS256 insertion sequence. Automated ribotyping has been shown to predict spa clonal complexes and MLST clonal complexes. The high cost and lower discriminatory power of automated ribotyping compared to spa and MSLT typing could be an obstacle to fine genotyping analyzes, especially when high discriminatory power is required. On the other hand, numerous advantages such as automation, ease and speed of execution, stability, typeability and reproducibility make ribotyping a reliable method to be juxtaposed to gold standard methods.

First records of Aedes pulcritarsis (Rondani, 1872) (Diptera: Culicidae) in Austria.

Aedes pulcritarsis is a tree-hole breeding species with its main distribution in the Mediterranean area. Within the scope of two independent monitoring programmes, this mosquito species was detected for the first time in Austria, in the province of Lower Austria (2018, districts Mistelbach and Gaenserndorf; 2020, district Bruck an der Leitha). As the climatic and habitat situation in Central Europe seems to be generally suitable for this species, the most likely explanation for the species not being recorded previously is that it might have been overlooked in the past due to its specialized breeding habitat. However, further research on the distribution of Ae. pulcritarsis in Austria would be needed to support this hypothesis. The results from this study will contribute to the investigation of the northern distribution limit of Ae. pulcritarsis in Europe and possible changes thereof.

Diversity of West Nile and Usutu virus strains in mosquitoes at an international airport in Austria.

Increased globalization and international transportation have resulted in the inadvertent introduction of exotic mosquitoes and new mosquito-borne diseases. International airports are among the possible points of entry for mosquitoes and their pathogens. We established a mosquito and mosquito-borne diseases monitoring programme at the largest international airport in Austria and report the results for the first two years, 2018 and 2019. This included weekly monitoring and sampling of adult mosquitoes, and screening them for the presence of viral nucleic acids by standard molecular diagnostic techniques. Additionally, we surveyed the avian community at the airport, as birds are potentially amplifying hosts. In 2018, West Nile virus (WNV) was detected in 14 pools and Usutu virus (USUV) was detected in another 14 pools of mosquitoes (minimum infection rate [MIR] of 6.8 for each virus). Of these 28 pools, 26 consisted of female Culex pipiens/torrentium, and two contained male Culex sp. mosquitoes. Cx. pipiens/torrentium mosquitoes were the most frequently captured mosquito species at the airport. The detected WNV strains belonged to five sub-clusters within the sub-lineage 2d-1, and all detected USUV strains were grouped to at least seven sub-clusters among the cluster Europe 2; all strains were previously shown to be endemic in Austria. In 2019, all mosquito pools were negative for any viral nucleic acids tested. Our study suggests that airports may serve as foci of arbovirus activity, particularly during epidemic years, and should be considered when designing mosquito control and arbovirus monitoring programmes.

The First Bacterial Endocarditis Due to Achromobacter xylosoxidans in a Dog.

Infectious endocarditis (IE) in dogs is often associated with a high mortality rate as diagnostic work-up as well as antibiotic treatment might be challenging. The present case describes bacteremia in a dog caused by Achromobacter xylosoxidans, leading to an infectious endocarditis. Achromobacter xylosoxidans (A. xylosoxidans) is an aerobic Gram-negative rod-shaped bacterium, which has been associated with multiple nosocomial opportunistic diseases in human medicine. One such manifestation of A. xylosoxidans infection is endocarditis. A. xylosoxidans infections are challenging to treat due to the reduced effectiveness of a wide range of antimicrobial agents. To date, only a few case reports of infections with A. xylosoxidans in animals have been described. This is the first case report of A. xylosoxidans endocarditis in a dog. Whole-genome sequencing was performed to determine the sequencing type and to gain more information about this bacterium regarding its intrinsic resistance genes. With this case report, we seek to increase awareness of A. xylosoxidans as an opportunistic nosocomial pathogen in dogs and to provide a short summary regarding the current state of general knowledge and known resistance patterns.

European Society of Clinical Microbiology and Infectious Diseases: 2021 update on the treatment guidance document for Clostridioides difficile infection in adults.

SCOPE: In 2009, the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) published the first treatment guidance document for Clostridioides difficile infection (CDI). This document was updated in 2014. The growing literature on CDI antimicrobial treatment and novel treatment approaches, such as faecal microbiota transplantation (FMT) and toxin-binding monoclonal antibodies, prompted the ESCMID study group on C. difficile (ESGCD) to update the 2014 treatment guidance document for CDI in adults. METHODS AND QUESTIONS: Key questions on CDI treatment were formulated by the guideline committee and included: What is the best treatment for initial, severe, severe-complicated, refractory, recurrent and multiple recurrent CDI? What is the best treatment when no oral therapy is possible? Can prognostic factors identify patients at risk for severe and recurrent CDI and is there a place for CDI prophylaxis? Outcome measures for treatment strategy were: clinical cure, recurrence and sustained cure. For studies on surgical interventions and severe-complicated CDI the outcome was mortality. Appraisal of available literature and drafting of recommendations was performed by the guideline drafting group. The total body of evidence for the recommendations on CDI treatment consists of the literature described in the previous guidelines, supplemented with a systematic literature search on randomized clinical trials and observational studies from 2012 and onwards. The Grades of Recommendation Assessment, Development and Evaluation (GRADE) system was used to grade the strength of our recommendations and the quality of the evidence. The guideline committee was invited to comment on the recommendations. The guideline draft was sent to external experts and a patients' representative for review. Full ESCMID endorsement was obtained after a public consultation procedure. RECOMMENDATIONS: Important changes compared with previous guideline include but are not limited to: metronidazole is no longer recommended for treatment of CDI when fidaxomicin or vancomycin are available, fidaxomicin is the preferred agent for treatment of initial CDI and the first recurrence of CDI when available and feasible, FMT or bezlotoxumab in addition to standard of care antibiotics (SoC) are preferred for treatment of a second or further recurrence of CDI, bezlotoxumab in addition to SoC is recommended for the first recurrence of CDI when fidaxomicin was used to manage the initial CDI episode, and bezlotoxumab is considered as an ancillary treatment to vancomycin for a CDI episode with high risk of recurrence when fidaxomicin is not available. Contrary to the previous guideline, in the current guideline emphasis is placed on risk for recurrence as a factor that determines treatment strategy for the individual patient, rather than the disease severity.

Draft Genome Sequence of a Multidrug-Resistant Escherichia coli Sequence Type 1193 Pandemic Clone Isolated from Wastewater in Austria.

Extraintestinal Escherichia coli sequence type 1193 (ST1193) is an important source of fluoroquinolone resistance, which has emerged in recent years. We report the first draft genome sequence and annotation of a multidrug-resistant E. coli ST1193 strain obtained from a wastewater treatment plant in Austria.