Test, test, test for COVID-19 antibodies: the importance of sensitivity, specificity and predictive powers.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody tests of varying specificity and sensitivity are now available. For informing individuals whether they have had coronavirus disease 2019 (COVID-19), they need to be very accurate. For measuring population prevalence of past infection, the numbers of false positives and negatives need to be roughly equal. With a series of worked examples for a notional population of 100,000 people, we show that even test systems with a high specificity can yield a large number of false positive results, especially where the population prevalence is low. For example, at a true population prevalence of 5%, using a test with 99% sensitivity and specificity, 16% of positive results will be false and thus 950 people will be incorrectly informed they have had the infection. Further confirmatory testing may be needed. Giving false reassurance on which personal or societal decisions might be based could be harmful for individuals, undermine public confidence and foster further outbreaks.

[Multidrug-resistant bacteria in animals and humans]. / Multiresistente Erreger bei Tier und Mensch.

BACKGROUND: The increasing burden of antimicrobial-resistant bacteria causes morbidity and mortality, especially among patients affected by healthcare-associated infections. Limited treatment options challenge clinicians in both human and veterinary medicine. OBJECTIVES: To summarize current evidence for the occurrence of antimicrobial-resistant bacteria and their zoonotic transmission between humans and animals with a focus on data from Germany. MATERIALS AND METHODS: Review of scientific literature and publications from German national public health institutions. RESULTS AND CONCLUSIONS: Methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum ß­lactamase (ESBL) producing Enterobacteriaceae are frequently transmitted between animals and humans. The rates of asymptomatic carriage are increased among persons with livestock contact compared with the general population. The occurrence of carbapenemase-producing Enterobacteriaceae has been documented on German pig and chicken farms, but investigations into their prevalence and zoonotic importance are pending. Colistin is frequently used in veterinary medicine to treat diarrhoea and causes selection pressure for colistin-resistant Gram-negative bacteria harbouring mcr genes. Vancomycin-resistant enterococci (VRE), oxazolidinone-resistant Gram-positive bacteria and multiresistant staphylococci are further antimicrobial-resistant microorganisms, which might have a zoonotic potential. Besides human healthcare and livestock, the problem of antimicrobial-resistant bacteria also affects companion animals (e. g. dogs, cats and horses), wildlife and the environment, which underlines the need to prevent antimicrobial resistance in a One Health approach.

Genotypic Characterization of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Isolates of Clonal Complex 398 in Pigsty Visitors: Transient Carriage or Persistence?

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) of clonal complex (CC) 398 has become a rising issue for public health. While it is known that >80% of pig farmers are colonized with LA-MRSA, only a few studies have assessed the situation for humans with occasional livestock contact. Recently it was shown that over 75% of scientific fieldworkers visiting pigsties were temporarily carrying LA-MRSA. To find out whether they were transiently or permanently colonized, we used whole-genome sequencing (WGS) data to analyze the relatedness of isolates from these recurrently LA-MRSA-positive fieldworkers and from corresponding pigsties. Sequences were analyzed using in silico typing (spa and core genomic multilocus sequence typing [cgMLST]), and the BEAST software package was used to examine phylogeny. In total, 81 samples from three fieldworkers on eight different pigsties over a period of 2.5 years were sequenced. All isolates belonged to spa type t011, t034, or t2011, with different types found in the same fieldworker at different time points. Analysis of cgMLST revealed nine genotypic clusters, mostly correlating with the pigsty on which they were sampled. Fieldworker isolates clustered with the samples from farms that were visited on the same day. BEAST analysis corroborated the cgMLST-based clustering and suggests an origin of the lineage about 22 years ago. We conclude that nasal LA-MRSA colonization among humans with occasional livestock contact is common but most likely only temporary. Furthermore, we showed that the Western German LA-MRSA CC398 originated in the late 1990s and diversified into farm-specific genotypes, which stay relatively consistent over time.

Searching for the source of Ebola: the elusive factors driving its spillover into humans during the West African outbreak of 2013-2016.

The natural ecology of Ebola virus infection remains enigmatic. No clear reservoir species has been confirmed but there is evidence of infection in a wide spectrum of mammals, including humans, non-human primates, domestic and wild ungulates and a variety of bat species, both frugivorous and insectivorous. Humans and most other species examined appear to be spillover hosts and suffer disease. Bats are the exception and are tolerant to infection in some laboratory studies. Some surveys show a low prevalence of antibodies against Zaire Ebola virus (ZEBOV) strains in bats during human outbreaks and inter-epidemic periods, and this order of mammals is considered to be the likely reservoir for the virus. Other putative sources include insects but this hypothesis is unproven in the field or laboratory. Moreover, some potential sources, such as aquatic species, have yet to be investigated. There are a number of environmental, human behavioural and ecological risk factors proposed with respect to spillover and spread. In the West African outbreak, which was unprecedented in scale and geographic spread, the source of the spillover remains unproven, although an association exists between the proposed index case and a colony of insectivorous bats. In all but a few Ebola virus disease events, spillover has only been superficially investigated and this was also the case in the West African epidemic. The authors suggest that, to address risks at the human-animal-environmental interface, using a One Health approach, more effort is needed to investigate spillover factors at the time of a ZEBOV epidemic, in addition to conducting inter-epidemic surveys in peridomestic environments. The true prevalence of ZEBOV infection in any species of bats remains unknown. Large-scale, expensive, non-randomised surveys, with low sampling numbers per species, are unlikely to provide evidence for Ebola virus reservoirs or to improve our epidemiological understanding.

L'écologie naturelle de l'infection par le virus Ebola demeure énigmatique. Si aucune espèce réservoir au sens strict n'a été clairement identifiée, le virus peut infecter un large spectre d'espèces de mammifères, parmi lesquelles l'être humain, des primates non humains, des ongulés domestiques et sauvages ainsi que de très nombreuses espèces de chauves-souris tant frugivores qu'insectivores. Les humains et la plupart des espèces animales étudiées semblent être des hôtes incidents chez qui la maladie se développe. Les chauves-souris constituent l'exception, certaines études de laboratoire ayant prouvé qu'elles sont tolérantes à l'infection. Des enquêtes ayant montré la présence d'anticorps dirigés contre les souches Zaïre du virus Ebola (Ebola-Zaïre) chez les chauves-souris, à un taux faible de prévalence, pendant les périodes d'activité des foyers chez l'homme ou dans les intervalles inter-épidémiques, cet ordre de mammifères est considéré comme un réservoir possible du virus. Les insectes constituent aussi des sources présumées mais cette hypothèse n'est pas encore démontrée sur le terrain ni même au laboratoire. D'autres sources potentielles doivent encore être étudiées, par exemple parmi les espèces aquatiques. Un certain nombre de facteurs de risque environnementaux, anthropiques et écologiques ont été proposés pour expliquer la transmission entre espèces et la propagation du virus. En ce qui concerne le foyer survenu en Afrique de l'Ouest, sans précédent par son ampleur et par son étendue géographique, la source de la transmission demeure inconnue bien qu'une corrélation ait été observée entre le cas index présumé et la présence d'une colonie de chauves-souris insectivores. Dans pratiquement tous les événements dus au virus Ebola (et l'épidémie en Afrique de l'Ouest ne fait pas exception), l'origine de la transmission n'a guère fait l'objet d'investigations approfondies. Pour que les risques à l'interface humains­ animaux­environnement puissent être traités selon la méthode Une seule santé, les auteurs estiment indispensable d'élucider au préalable les facteurs de transmission qui ont pu intervenir lors des épidémies dues au virus Ebola-Zaïre, en plus des enquêtes à effectuer entre deux épidémies et dans un environnement péridomestique. Nous ignorons encore quelle est la prévalence réelle de l'infection par le virus EbolaZaïre chez les chauves-souris, toutes espèces confondues. Il est peu probable que des enquêtes à grande échelle, onéreuses et basées sur des échantillons non aléatoires constitués d'un faible nombre d'individus par espèce parviennent à identifier les réservoirs du virus Ebola ou à améliorer nos connaissances sur son épidémiologie.

La ecología natural de la infección por el virus del Ebola sigue siendo enigmática. No hay especie en la que esté probada una clara función de reservorio, aunque existen datos demostrativos de infección en muy diversos mamíferos, como el ser humano, primates no humanos, ungulados domésticos y silvestres y varias especies de murciélago, tanto frugívoras como insectívoras. El ser humano y la mayoría de las especies estudiadas parecen ser hospedadores no preferentes y padecer la enfermedad, con la única excepción de los murciélagos, que a tenor de ciertos estudios de laboratorio son tolerantes a la infección. En estos animales, algunas investigaciones realizadas sobre el terreno muestran una baja prevalencia de anticuerpos contra cepas de la especie Zaire del virus durante los brotes de infección en el hombre y en los periodos interepidémicos, y se considera probable que este orden de mamíferos sea el reservorio del virus. Se presume que otra fuente podrían ser los insectos, pero ni los datos de laboratorio ni los obtenidos sobre el terreno avalan por ahora tal hipótesis. Además, aún hay otras posibles fuentes por estudiar, como ciertas especies acuáticas. Con respecto a la extensión secundaria y la propagación del virus se han apuntado una serie de posibles factores de riesgo de índole ambiental o ecológica o ligados al comportamiento humano. En el caso del brote habido en África Occidental, que revistió una escala y un alcance geográfico sin precedentes, no se ha demostrado aún cuál fue la fuente de la extensión secundaria, aunque existe una relación entre el caso índice propuesto y una colonia de murciélagos insectívoros. En casi todos los episodios de enfermedad por el virus del Ebola la extensión secundaria se ha investigado solo de forma superficial, como también fue el caso de la epidemia de África Occidental. Los autores sugieren que, para abordar los riesgos existentes en la interfaz del ser humano, los animales y el medio ambiente en clave de Una sola salud, es preciso investigar más a fondo los factores que inducen la extensión secundaria durante una epidemia del virus Zaire del Ebola, además de efectuar estudios del medio peridoméstico en las fases interepidémicas. En ninguna especie de murciélago se conoce aún la verdadera prevalencia de la infección por el virus Zaire. Es poco probable que la realización de onerosos estudios no aleatorizados a gran escala, con la obtención de un pequeño número de muestras por especie, depare indicios sólidos en cuanto a los reservorios del virus del Ebola o nos sirva para entender mejor su epidemiología.

Cross-border comparison of antimicrobial resistance (AMR) and AMR prevention measures: the healthcare workers' perspective.

Background: Cross-border healthcare may promote the spread of multidrug-resistant microorganisms (MDRO) and is challenging due to heterogeneous antimicrobial resistance (AMR) prevention measures (APM). The aim of this article is to compare healthcare workers (HCW) from Germany (DE) and The Netherlands (NL) on how they perceive and experience AMR and APM, which is important for safe patient exchange and effective cross-border APM cooperation. Methods: A survey was conducted amongst HCW (n = 574) in hospitals in DE (n = 305) and NL (n = 269), using an online self-administered survey between June 2017 and July 2018. Mann-Whitney U tests were used to analyse differences between answers of German and Dutch physicians (n = 177) and German and Dutch nurses (n = 397) on 5-point Likert Items and Scales. Results: Similarities between DE and NL were a high awareness about the AMR problem and the perception that the possibility to cope with AMR is limited (30% respondents perceive their contribution to limit AMR as insufficient). Especially Dutch nurses scored significantly lower than German nurses on their contribution to limit AMR (means 2.6 vs. 3.1, p ≤ 0.001). German HCW were more optimistic about their potential role in coping with AMR (p ≤ 0.001), and scored higher on feeling sufficiently equipped to perform APM (p ≤ 0.003), although the mean scores did not differ much between German and Dutch respondents. Conclusions: Although both German and Dutch HCW are aware of the AMR problem, they should be more empowered to contribute to limiting AMR through APM (i.e. screening diagnostics, infection diagnosis, treatment and infection control) in their daily working routines. The observed differences reflect differences in local, national and cross-border structures, and differences in needs of HCW, that need to be considered for safe patient exchange and effective cross-border APM.

Correction to: Cross-border comparison of antimicrobial resistance (AMR) and AMR prevention measures: the healthcare workers' perspective.

[This corrects the article DOI: 10.1186/s13756-019-0577-4.].

Acquisition and colonization dynamics of antimicrobial-resistant bacteria during international travel: a prospective cohort study.

OBJECTIVES: Travellers may be colonized with antimicrobial-resistant bacteria on return, but little is known about colonization during travel. Our objectives were to assess the acquisition and colonization dynamics during the stay abroad for a broad range of antimicrobial-resistant bacteria and resistance phenotypes and to identify risk factors for faecal carriage of antimicrobial-resistant bacteria. METHODS: German and Dutch participants (n = 132) of this prospective cohort study (2016-2018) completed a questionnaire on risk factors and provided daily stool samples before, during, and after travel. Samples were screened for extended-spectrum ß-lactamase producing Enterobacterales (ESBL-E), carbapenem-resistant (CarbR-GN), and non-intrinsically colistin-resistant Gram-negative rods (ColR-GN), vancomycin-resistant Enterococcus faecium/faecalis (VRE), and Clostridioides difficile. RESULTS: Colonization rates reached a plateau within a week after departure fluctuating around 48.5% (63/130) and 58.4% (45/77, ESBL-E), 10.4% (11/106) and 23.4% (18/77, ColR-GN), or 3.0% (4/132) and 6.8% (8/118, CarbR-GN). Colonization rates after the travel were 46.2% (61/132, ESBL-E), 9.0% (12/132, ColR-GN), and 3.4% (5/132, CarbR-GN). Travellers carried mcr-1- (15/132; 11.4%) or blaNDM-positive (4/132; 3.0%) Enterobacterales. A vegetarian diet was associated with a lower risk for the acquisition of ESBL-E (OR = 0.4, p 0.04) and ColR-GN (OR = 0.1, p 0.01) during travel in a multivariable model. Similarly, travellers visiting friends and relatives had a lower risk for the acquisition of ESBL-E (OR = 0.3, p 0.009) and CarbR-GN (OR = 0.3, p 0.01). VRE and C. difficile were not detected. CONCLUSION: The number of travellers with a temporary colonization during the journey exceeded the number of travellers still colonized after return.

Carbapenem-resistant Enterobacteriaceae in wildlife, food-producing, and companion animals: a systematic review.

OBJECTIVES: The spread of carbapenem-resistant Enterobacteriaceae (CRE) in healthcare settings challenges clinicians worldwide. However, little is known about dissemination of CRE in livestock, food, and companion animals and potential transmission to humans. METHODS: We performed a systematic review of all studies published in the PubMed database between 1980 and 2017 and included those reporting the occurrence of CRE in samples from food-producing and companion animals, wildlife, and exposed humans. The primary outcome was the occurrence of CRE in samples from these animals; secondary outcomes included the prevalence of CRE, carbapenemase types, CRE genotypes, and antimicrobial susceptibilities. RESULTS: We identified 68 articles describing CRE among pigs, poultry, cattle, seafood, dogs, cats, horses, pet birds, swallows, wild boars, wild stork, gulls, and black kites in Africa, America, Asia, Australia, and Europe. The following carbapenemases have been detected (predominantly affecting the genera Escherichia and Klebsiella): VIM, KPC, NDM, OXA, and IMP. Two studies found that 33-67% of exposed humans on poultry farms carried carbapenemase-producing CRE closely related to isolates from the farm environment. Twenty-seven studies selectively screened samples for CRE and found a prevalence of <1% among livestock and companion animals in Europe, 2-26% in Africa, and 1-15% in Asia. Wildlife (gulls) in Australia and Europe carried CRE in 16-19%. CONCLUSIONS: The occurrence of CRE in livestock, seafood, wildlife, pets, and directly exposed humans poses a risk for public health. Prospective prevalence studies using molecular and cultural microbiological methods are needed to better define the scope and transmission of CRE.

In the centre of an epidemic: Fifteen years of LA-MRSA CC398 at the University Hospital Münster.

Ten years after initial publications on livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) in 2005, we report on the course of the LA-MRSA CC398 epidemic among patients of the University Hospital Münster. This tertiary care facility is located in the Dutch-German border region (EUREGIO), which is characterized by a high density of livestock production and is hence a hotspot for the occurrence of LA-MRSA CC398. Taking advantage of the unique opportunity to track the emergence and spread of MRSA CC398 among humans from the very beginning of the epidemic until today, a total of 6555 non-duplicate MRSA isolates from all screenings and clinical specimens cultivated within the period from 2000 to 2014 were included in the analysis. Retrospectively, the first MRSA CC398 isolate (spa type t034) was obtained from a screening specimen of a patient in 2000, which represents one of the first human-associated LA-MRSA CC398 isolates reported in Europe. After sporadic detections between 2000 and 2004, this clonal lineage accounted for 9.6% of all local MRSA in 2005; a proportion which increased to 35% in 2013 and became stable since then. Considering the period from 2000 to 2014, the group of MRSA CC398 isolates comprised a total of 45 different spa types among which t011 (48.3%), t034 (39.3%) and t108 (3.5%) were predominant and so far unreported types were found. Overall, LA-MRSA CC398 emerged rapidly during the past decade, developed enormous sublineage diversity and contributed substantially to the total burden of MRSA colonization and infection at the hospital.

Persistence of nasal colonization with human pathogenic bacteria and associated antimicrobial resistance in the German general population.

The nares represent an important bacterial reservoir for endogenous infections. This study aimed to assess the prevalence of nasal colonization by different important pathogens, the associated antimicrobial susceptibility and risk factors. We performed a prospective cohort study among 1878 nonhospitalized volunteers recruited from the general population in Germany. Participants provided nasal swabs at three time points (each separated by 4-6 months). Staphylococcus aureus, Enterobacteriaceae and important nonfermenters were cultured and subjected to susceptibility testing. Factors potentially influencing bacterial colonization patterns were assessed. The overall prevalence of S. aureus, Enterobacteriaceae and nonfermenters was 41.0, 33.4 and 3.7%, respectively. Thirteen participants (0.7%) were colonized with methicillin-resistant S. aureus. Enterobacteriaceae were mostly (>99%) susceptible against ciprofloxacin and carbapenems (100%). Extended-spectrum ß-lactamase-producing isolates were not detected among Klebsiella oxytoca, Klebsiella pneumoniae and Escherichia coli. Several lifestyle- and health-related factors (e.g. household size, travel, livestock density of the residential area or occupational livestock contact, atopic dermatitis, antidepressant or anti-infective drugs) were associated with colonization by different microorganisms. This study unexpectedly demonstrated high nasal colonization rates with Enterobacteriaceae in the German general population, but rates of antibiotic resistance were low. Methicillin-resistant S. aureus carriage was rare but highly associated with occupational livestock contact.

Low-level antimicrobial resistance of Enterobacteriaceae isolated from the nares of pig-exposed persons.

Extended-spectrum ß-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) have recently emerged in livestock and humans. Therefore, this study assessed the carriage of Enterobacteriaceae in the anterior nares and associated antimicrobial resistance in pig-exposed persons. Nasal swabs were enriched in non-selective broth and then plated on MacConkey and ESBL-selective agars. Species was confirmed by matrix-assisted laser-desorption ionization-time-of-flight mass spectrometry (MALDI-ToF MS). Antimicrobial susceptibility testing was performed according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. Of 114 pig-exposed persons tested, Enterobacteriaceae were detected in the nares of 76 (66·7%) participants. The predominant species were Proteus mirabilis (n = 17, 14·9%), Pantoea agglomerans (n = 13, 11·4%), Morganella morganii (n = 9, 7·9%), Citrobacter koseri (n = 9, 7·9%), Klebsiella pneumoniae, Escherichia coli and Proteus vulgaris (each n = 8, 7·0%). ESBL-E were not detected. Of all isolates tested, 3·4% were resistant against ciprofloxacin, 2·3% against gentamicin, 23·9% against trimethoprim-sulfamethoxazole and 44·3% against tigecycline. Despite the high prevalence of ESBL-E in livestock, pig-exposed persons did not carry ESBL-E in their nares. This finding is important, because colonization of the nasal reservoir might cause endogenous infections or facilitate transmission of ESBL-E in the general population.

Vertebrate reservoirs and secondary epidemiological cycles of vector-borne diseases.

Vector-borne diseases of importance to human and domestic animal health are listed and the increasing emergence of syndromes, new epidemiological cycles and distributions are highlighted. These diseases involve a multitude of vectors and hosts, frequently for the same pathogen, and involve natural enzootic cycles, wild reservoirs and secondary epidemiological cycles, sometimes affecting humans and domestic animals. On occasions the main reservoir is in the domestic environment. Drivers for secondary cycles are mainly related to human impacts and activities and therefore, for purposes of prevention and control, the focus needs to be on the socioecology of the diseases. Technical and therapeutical solutions exist, and for control there needs to be a clear understanding of the main vertebrate hosts or reservoirs and the main vectors. The targets of interventions are usually the vector and/or secondary epidemiological cycles and, in the case of humans and domestic animals, the spillover or incidental hosts are treated. More attention needs to be given to the importance of the political economy in relation to vector-borne diseases, as many key drivers arise from globalisation, climate change and changes in structural ecologies. Attention to reducing the risk of emergence of new infection cycles through better management of the human-animal-environment interface is urgently needed.

Detection and Genetic Characterization of Lineage IV Peste Des Petits Ruminant Virus in Kazakhstan.

Peste des petits ruminant (PPR) is endemic in many Asian countries with expansion of the range in recent years including across China during 2013-2014 (OIE, 2014). Till the end of 2014, no cases of PPR virus (PPRV) were officially reported to the Office Internationale des Epizooties (OIE) from Kazakhstan. This study describes for the first time clinicopathological, epidemiological and genetic characterization of PPRV in 3 farm level outbreaks reported for the first time in Zhambyl region (oblast), southern Kazakhstan. Phylogenetic analysis based on partial N gene sequence data confirms the lineage IV PPRV circulation, similar to the virus that recently circulated in China. The isolated viruses are 99.5-99.7% identical to the PPRV isolated in 2014 from Heilongjiang Province in China and therefore providing evidence of transboundary spread of PPRV. There is a risk of further maintenance of virus in young stock despite vaccination of adult sheep and goats, along livestock trade and pastoral routes, threatening both small livestock and endangered susceptible wildlife populations throughout Kazakhstan.

State-wide surveillance of antibiotic resistance patterns and spa types of methicillin-resistant Staphylococcus aureus from blood cultures in North Rhine-Westphalia, 2011-2013.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of bacteraemia. We aimed to obtain a complete picture of severe MRSA infections by characterizing all MRSA isolates from bloodstream infections in the largest German federal state (North Rhine-Westphalia, 18 million inhabitants) using S. aureus protein A (spa) sequence-typing and antimicrobial susceptibility testing. MRSA isolates (n = 1952) were collected prospectively (2011-2013) and spa-typed. Among 181 different spa types, t003 (n = 746 isolates; 38.2%) and t032 (n = 594; 30.4%) were predominant. Analysis of the geographical occurrence of spa clonal complexes (spa-CCs) and spa types revealed divergent distribution between federal state districts for spa-CCs 003 (p < 0.001; including t003, p < 0.001 and t264, p < 0.001), 008 (p 0.021), 011 (p 0.002), 032 (p < 0.001; including t022, p 0.014 and t032, p < 0.001) and spa type t2807 (p < 0.001). MICs of antimicrobial substances were tested using broth microdilution. Of all isolates, 96% were resistant to fluoroquinolones, 78% to erythromycin, 70% to clindamycin, 4% to gentamicin, 2% to rifampicin, 0.4% to daptomycin, 0.1% to linezolid and 0% to vancomycin, respectively. Vancomycin MICs of 2 mg/L involved 0.5% of the isolates. In conclusion, the detection of regional molecular clusters added valuable information for epidemiological case tracing and allowed conclusions to be reached on the importance of newly emerging MRSA reservoirs, such as livestock (spa-CC011), for MRSA bacteraemia in some parts of the federal state. Susceptibility testing revealed broad resistance to substances used for oral treatment, but demonstrated that those antibiotics that are mostly applied for treatment of MRSA bacteraemia and important combination partners were highly susceptible.