Multiple Outbreaks Research Articles

CRISPR-Cas13 as an Antiviral Strategy for Coronavirus Disease 2019.

CRISPR-Cas13 as an Antiviral Strategy for Coronavirus Disease 2019.

Tu1036 RISK ESTIMATE OF DUODENOSCOPE-ASSOCIATED INFECTIONS (DAI) IN THE NETHERLANDS

The likelihood of endoscopy-associated infections (EAI) is often referenced from a paper published in 1993 by Kimmery and co-workers in which a risk of 1 exogenous infection for every 1.8 million endoscopies (0,00006%) is proclaimed.(1) Even though Ofstead et al.(2) pointed out in 2013 that this was at least an underestimation by 6-fold because of erroneous assumptions and mathematical errors, the original calculation is still often referred to. In the past decade, multiple outbreaks of multi-resistant microorganisms (MDRO) related to contaminated duodenoscopes have been reported worldwide. This leads to the assumption that the former risk calculation is indeed incorrect. The aim of our study is to calculate the duodenoscope-associated infection (DAI) risk for the Dutch ERCP practice. We searched and consolidated all Dutch patients reported in the literature to have suffered from a clinical infection linked to a contaminated duodenoscope between 2008 and 2018. From a national database the number of ERCP's performed per year in the Netherlands were retrieved. Actual numbers were available from 2012 to 2018. Numbers from 2008 to 2011 were estimated and assumed to be equal to 2012. In the period 2008 to 2018, three MDRO outbreaks in Dutch hospitals were reported in the literature with 21 patients suffering from a clinical infection based on a microorganism proven to be transmitted by a duodenoscope. In that time period, approximately 203.500 ERCP procedures were performed. Hence, for every 1 out of 9690 procedures one patient developed a clinically relevant infection amounting to a DAI risk of 0.010%. The risk of developing a DAI is at least 30 to 180 times higher than the risks that were previously reported for all types of endoscopy-associated infections. Importantly, the current calculated risk of 0.010% constitutes a bare minimum risk of DAI because endoscope related infections are under-reported. Apart from DAI risk there is also the risk of patients becoming colonized with MO through contaminated endoscopes but without developing symptoms of a clinical infection. These data call for consorted action of medical practitioners, industry and government agencies to minimize and ultimately ban the risk of exogenous endoscope associated infections and contamination. As a first step, the FDA recently recommended health care facilities and manufacturers begin transitioning to duodenoscopes with disposable components.

Mapping Multiple Insect Outbreaks across Large Regions Annually Using Landsat Time Series Data

Forest insect outbreaks have caused and will continue to cause extensive tree mortality worldwide, affecting ecosystem services provided by forests. Remote sensing is an effective tool for detecting and mapping tree mortality caused by forest insect outbreaks. In this study, we map insect-caused tree mortality across three coniferous forests in the Western United States for the years 1984 to 2018. First, we mapped mortality at the tree level using field observations and high-resolution multispectral imagery collected in 2010, 2011, and 2018. Using these high-resolution maps of tree mortality as reference images, we then classified moderate-resolution Landsat imagery as disturbed or undisturbed and for disturbed pixels, predicted percent tree mortality with random forest (RF) models. The classification approach and RF models were then applied to time series of Landsat imagery generated with Google Earth Engine (GEE) to create annual maps of percent tree mortality. We separated disturbed from undisturbed forest with overall accuracies of 74% to 80%. Cross-validated RF models explained 61% to 68% of the variation in percent tree mortality within disturbed 30-m pixels. Landsat-derived maps of tree mortality were comparable to vector aerial survey data for a variety of insect agents, in terms of spatial patterns of mortality and annual estimates of total mortality area. However, low-level tree mortality was not always detected. We conclude that our methodology has the potential to generate reasonable estimates of annual tree mortality across large extents.

Emergence of Enteroaggregative Escherichia coli within the ST131 Lineage as a Cause of Extraintestinal Infections.

Escherichia coli sequence type 131 (ST131) is a major cause of urinary and bloodstream infections. Its association with extended-spectrum β-lactamases (ESBLs) significantly complicates treatment. Its best-described component is the rapidly expanding H30Rx clade, containing allele 30 of the type 1 fimbrial adhesin gene fimH This lineage appears to have emerged in the United States and spread around the world in part due to the acquisition of the ESBL-encoding blaCTX-M-15 gene and resistance to fluoroquinolones. However, non-H30 ST131 sublineages with other acquired CTX-M-type resistance genes are also emerging. Based on whole-genome analyses, we describe here the presence of an (fimH) H27 E. coli ST131 sublineage that has recently caused an outbreak of community-acquired bacteremia and recurrent urinary tract infections (UTIs) in Denmark. This sublineage has acquired both a virulence plasmid (pAA) that defines the enteroaggregative E. coli (EAEC) diarrheagenic pathotype and multiple genes associated with extraintestinal E. coli (ExPEC); combined, these traits have made this particular ST131 sublineage successful at colonizing its human host and causing recurrent UTI. Moreover, using a historic World Health Organization (WHO) E. coli collection and publicly available genome sequences, we identified a global H27 EAEC ST131 sublineage that dates back as far as 1998. Most H27 EAEC ST131 isolates harbor pAA or pAA-like plasmids, and our analysis strongly implies a single ancestral acquisition among these isolates. These findings illustrate both the profound plasticity of this important pathogenic E. coli ST131 H27 sublineage and genetic acquisitions of EAEC-specific virulence traits that likely confer an enhanced ability to cause intestinal colonization.IMPORTANCEE. coli ST131 is an important extraintestinal pathogenic lineage. A signature characteristic of ST131 is its ability to asymptomatically colonize the gastrointestinal tract and then opportunistically cause extraintestinal infections, such as cystitis, pyelonephritis, and urosepsis. In this study, we identified an ST131 H27 sublineage that has acquired the enteroaggregative diarrheagenic phenotype, spread across multiple continents, and caused multiple outbreaks of community-acquired ESBL-associated bloodstream infections in Denmark. The strain's ability to both cause diarrhea and innocuously colonize the human gastrointestinal tract may facilitate its dissemination and establishment in the community.

COVID-19 outbreak: The early response of a UK orthopaedic department

COVID-19 outbreak: The early response of a UK orthopaedic department

Notes from the Field: Multiple Cruise Ship Outbreaks of Norovirus Associated with Frozen Fruits and Berries - United States, 2019.

This investigation highlights the importance of acute gastroenteritis (AGE) surveillance at sea to identify contaminated foods at sea not yet implicated on land and to prevent transmission of AGE illness through U.S. ports.

Ecological Niche Models of Four Hard Tick Genera (Ixodidae) in Mexico.

Simple SummaryVector-borne diseases currently represent a significant threat to public health, mainly due to the changes that humans are producing in ecosystems and climates. Analyzing the environmental conditions that allow the establishment and survival of ticks could help determine possible sites for the appearance of infectious outbreaks. In this study, nine ecological niche models were generated from different algorithms to determine the current potential distribution of four tick genera in Mexico. Temperature and moisture have been considered as the main factors limiting tick distribution. However, the analysis of the ecological niche models determined that the four genera exhibited different distribution patterns, which may be associated with their physiological and ecological differences. This type of analysis can improve our understanding of the dynamics of ticks and, therefore, can be very useful in monitoring programs of the diseases they transmit.Ticks are vectors of a large number of pathogens of medical and veterinary importance, and in recent years, they have participated in the rise of multiple infectious outbreaks around the world. Studies have proposed that temperature and precipitation are the main variables that limit the geographical distribution of ticks. The analysis of environmental constraints with ecological niche modeling (ENM) techniques can improve our ability to identify suitable areas for emergence events. Algorithms used in this study showed different distributional patterns for each tick genera; the environmental suitability for Amblyomma includes warm and humid localities below 1000 m above the sea level, while Ixodes is mainly associated with ecosystems with high vegetation cover. Dermacentor and Rhipicephalus genus presented wider distribution patterns; the first includes species that are well adapted to resist desiccation, whereas the latter includes generalist species that are mostly associated with domestic hosts in Mexico. Ecological niche models have proven to be useful in estimating the geographic distribution of many taxa of ticks. Despite our limited knowledge of tick’s diversity, ENM can improve our understanding of the dynamics of vector-borne diseases and can assist public health decision-making processes.

COVID-19: emergency medicine perspectives from Hong Kong.

COVID-19: emergency medicine perspectives from Hong Kong.

Ensuring global access to COVID-19 vaccines

Ensuring global access to COVID-19 vaccines

Draft Genome Sequences of 26 Salmonella Isolates Associated with Multiple Outbreaks in Brazil.

Salmonella enterica subsp. enterica isolates are the leading cause of foodborne illness worldwide. Here, we report the draft genomes of 26 Salmonella isolates of food and clinical origin, belonging to four serovars, associated with outbreaks from 1999 to 2006 in the south of Brazil.

Draft Genome Sequences of 30 Salmonella enterica Serovar Enteritidis Isolates Associated with Multiple Outbreaks in Brazil.

Salmonella enterica subsp. enterica serovar Enteritidis has been the prevalent serovar isolated from gastroenteritis cases in Brazil since the 1990s. Here, we report the draft genomes of 30 S Enteritidis isolates originating from a variety of patients and implicated foods during outbreaks between 1999 and 2006 in Brazil.

Molecular typing of Cyclospora cayetanensis in produce and clinical samples using targeted enrichment of complete mitochondrial genomes and next-generation sequencing

BackgroundOutbreaks of cyclosporiasis, a diarrheal illness caused by Cyclospora cayetanensis, have been a public health issue in the USA since the mid 1990’s. In 2018, 2299 domestically acquired cases of cyclosporiasis were reported in the USA as a result of multiple large outbreaks linked to different fresh produce commodities. Outbreak investigations are hindered by the absence of standardized molecular epidemiological tools for C. cayetanensis. For other apicomplexan coccidian parasites, multicopy organellar DNA such as mitochondrial genomes have been used for detection and molecular typing.MethodsWe developed a workflow to obtain complete mitochondrial genome sequences from cilantro samples and clinical samples for typing of C. cayetanensis isolates. The 6.3 kb long C. cayetanensis mitochondrial genome was amplified by PCR in four overlapping amplicons from genomic DNA extracted from cilantro, seeded with oocysts, and from stool samples positive for C. cayetanensis by diagnostic methods. DNA sequence libraries of pooled amplicons were prepared and sequenced via next-generation sequencing (NGS). Sequence reads were assembled using a custom bioinformatics pipeline.ResultsThis approach allowed us to sequence complete mitochondrial genomes from the samples studied. Sequence alterations, such as single nucleotide polymorphism (SNP) profiles and insertion and deletions (InDels), in mitochondrial genomes of 24 stool samples from patients with cyclosporiasis diagnosed in 2014, exhibited discriminatory power. The cluster dendrogram that was created based on distance matrices of the complete mitochondrial genome sequences, indicated distinct strain-level diversity among the 2014 C. cayetanensis outbreak isolates analyzed in this study.ConclusionsOur results suggest that genomic analyses of mitochondrial genome sequences may help to link outbreak cases to the source.

Covid-19 spreads in US.

Multiple outbreaks worldwide have led to countries stepping up their responses. By Debora MacKenzie and Press Association

Epidemiology of colistin-resistant, carbapenemase-producing Enterobacteriaceae and Acinetobacter baumannii in Croatia

Colistin is a last-resort antibiotic for the treatment of infections caused by multidrug and carbapenem-resistant Gram-negative bacteria. Colistin resistance has been emerging and multiple outbreaks have been reported in Europe and elsewhere. It has been most frequently reported in carbapenem-resistant K. pneumoniae. In this study, 24 multidrug and colistin-resistant clinical isolates (14 K. pneumoniae, one E. aerogenes, one E. cloacae, and eight A. baumannii) were collected from four hospitals in Croatia from 2013 to 2018, in order to analyse the molecular epidemiology and mechanisms of antibiotic resistance. β-lactamase and carbapenemase genes were detected by PCR. Genotyping was done on selected isolates by rep-PCR. Whole genome sequencing (WGS) was performed to discover possible molecular mechanisms for the observed colistin resistance. All isolates, except two K. pneumoniae isolates, were extensively drug resistant. Ten out of 16 (63%) K. pneumoniae isolates possessed blaOXA-48, which is the most common carbapenem resistance gene in Croatia and in other parts of Europe. All A. baumannii isolates possessed the OXA-23-like carbapenem hydrolysing oxacillinase and five turned out to be pandrug-resistant. Colistin resistance was most likely chromosomally mediated. After sequence analysis, none of the isolates were found to possess any of the mcr gene variants. Several previously reported mutations were found in PmrB, PhoP, PhoQ, and MgrB, which are associated with colistin resistance. In the global phylogenetic analysis, DNA mutations causing mutations in the MgrB protein were present mostly in lineages comprising colistin resistant isolates, and the second most prevalent mutation (K3X) was also encountered in our isolates. In addition, based on genotyping by rep-PCR, the spread of colistin resistance is most likely to be clonal. Most importantly, the presence of colistin resistance together with carbapenemase genes in extensively drug resistant isolates poses real threats in the use of carbapenems and colistin to fight infections.

Viral nervous necrosis outbreaks caused by the RGNNV/SJNNV reassortant betanodavirus in gilthead sea bream (Sparus aurata) and European sea bass (Dicentrarchus labrax)

Mediterranean marine aquaculture has suffered significant economic losses due to viral nervous necrosis (VNN) outbreaks mainly caused by different RGNNV betanodavirus strains. In recent years, the marine aquaculture sector has experienced the emergence of the RGNNV/SJNNV reassortant betanodavirus, harbouring the RNA1 segment of RGNNV genotype and the RNA2 segment of SJNNV genotype. So far, the reassortant strains caused massive mortality outbreaks in gilthead sea bream (Sparus aurata) larvae sparing the European sea bass (Dicentrarchus labrax). In this study, multiple mortality outbreaks occurred in one Italian marine hatchery involving both European sea bass and gilthead sea bream at different life stages were investigated through a complete microbiological and molecular analysis. Gilthead sea bream larvae and juveniles have recorded the highest mortality rates, however, both European sea bass and gilthead sea bream incurred a RGNNV/SJNNV reassortant betanodavirus persistent infection, able to act as asymptomatic carriers and viral source for susceptible fish. These new epidemiological data on nervous necrosis virus (NNV) reassortant infection provide precious advice on how to manage fish to reduce VNN spread in Mediterranean aquaculture. Evidence of interspecies transmission of RGNNV/SJNNV reassortant strains and the persistent infection in both European sea bass and gilthead sea bream, point out the importance to enforce a wide surveillance and a strict biosecurity programme addressing both RGNNV and reassortant RGNNV/SJNNV betanodaviruses in Mediterranean European sea bass and gilthead sea bream farms. Furthermore, the presence assessment of betanoviruses in all newly-introduced fish batches in the farm, regardless of the species and a strict segregation between European sea bass and gilthead sea bream batches within farms can significantly reduce the risk of NNV transmission. Finally, surviving fish can act as carrier fish, and thereby must be segregated from other batches and protected from stress conditions that could trigger a new clinical phase.

High risk for human exposure to Rift Valley fever virus in communities living along livestock movement routes: Across-sectional survey in Kenya.

IntroductionMultiple outbreaks of Rift Valley Fever (RVF) with devastating effects have occurred in East Africa. These outbreaks cause disease in both livestock and humans and affect poor households most severely. Communities living in areas practicing nomadic livestock movement may be at higher risk of infection. This study sought to i) determine the human exposure to Rift Valley fever virus (RVFV) in populations living within nomadic animal movement routes in Kenya; and ii) identify risk factors for RVFV infection in these communities.MethodsA cross-sectional descriptive study design was used. Samples were collected from the year 2014 to 2015 in a community-based sampling exercise involving healthy individuals aged ≥18 years from Isiolo, Tana River, and Garissa counties. In total, 1210 samples were screened by ELISA for the presence of immunoglobulin IgM and IgG antibodies against RVFV. Positive results were confirmed by plaque reduction neutralization test.ResultsOverall, IgM and IgG prevalence for all sites combined was 1.4% (95% CI 0.8–2.3%) and 36.4% (95% CI 33.8–39.2%), respectively. Isiolo County recorded a non-significant higher IgG prevalence of 38.8% than Garissa 35.9% and Tana River 32.2% (Chi square = 2.5, df = 2, p = 0.287). Males were significantly at higher risk of infection by RVFV than females (OR = 1.67, 95% CI 1.17–2.39, p<0.005). Age was significantly associated with RVFV infection (Wald Chi = 94.2, df = 5, p<0.0001). Individuals who had regular contact with cattle (OR = 1.38, 95%CI 1.01–1.89) and donkeys (OR = 1.38, 95%CI 1.14–1.67), or contact with animals through birthing (OR = 1.69, 95%CI 1.14–2.51) were significantly at a greater risk of RVFV infection than those who did not.ConclusionThis study demonstrated that although the Isiolo County has been classified as being at medium risk for RVF, virus infection appeared to be as prevalent in humans as in Tana River and Garissa, which have been classified as being at high risk. Populations in these counties live within nomadic livestock movement routes and therefore at risk of being exposed to the RVFV. Interventions to control RVFV infections therefore, should target communities living along livestock movement pathways.

Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017.

In 2017, the US Food and Drug Administration investigated the sources of multiple outbreaks of salmonellosis. Epidemiologic and traceback investigations identified Maradol papayas as the suspect vehicles. During the investigations, the genomes of 55 Salmonella enterica that were isolated from papaya samples were sequenced. Serovar assignments and phylogenetic analysis placed the 55 isolates into ten distinct groups, each representing a different serovar. Within-serovar SNP differences are generally between 0 and 20 SNPs, while the median between-serovar distance is 51 812 SNPs. We observed two groups with SNP distances between 21 and 100 SNPs. These relatively large within-serovar SNP distances may indicate that the isolates represent either diverse populations or multiple, genetically distinct subpopulations. Further inspection of these cases with traceback evidence allowed us to identify an 11th population. We observed that high levels of genomic diversity from individual firms is possible, with one firm yielding five of the ten serovars. Also, high levels of diversity are possible within small geographic regions, as five of the serovars were isolated from papayas that originated from farms located in Armería and Tecomán, Colima. In addition, we identified AMR genes that are present in three of the serovars studied here (aph(3')-lb, aph(6)-ld, tet(C), fosA7, and qnrB19) and we detected the presence of the plasmid IncHI2A among S. Urbana isolates.

Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit

We observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections at a Dutch neonatal intensive care unit. Weekly neonatal MSSA carriage surveillance and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. Traditional clustering of MSSA isolates by spa typing and Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections. We investigated whether whole-genome sequencing (WGS) of MSSA surveillance would provide additional evidence for transmission. MSSA isolates from neonatal infections, carriage surveillance, and HCWs were subjected to WGS and bioinformatic analysis for identification and localization of high-quality single nucleotide polymorphisms, and in-depth analysis of subsets of isolates. By measuring the genetic diversity in background surveillance, we defined transmission-level relatedness and identified isolates that had been unjustly assigned to clusters based on MLVA, while spa typing was concordant but of insufficient resolution. Detailing particular subsets of isolates provided evidence that HCWs were involved in multiple outbreaks, yet it alleviated concerns about one particular HCW. The improved resolution and accuracy of genomic outbreak analyses substantially altered the view on outbreaks, along with apposite measures. Therefore, inclusion of the circulating background population has the potential to overcome current issues in genomic outbreak inference.

Immunopathology of Zika virus infection.

Zika virus (ZIKV) is a mosquito-borne virus of the flavivirus genus in the Flaviviridae family. Flaviviruses are single-stranded, positive-sense RNA viruses that have been responsible for numerous human epidemics. Notable flaviviruses include mosquito-borne viruses such as yellow fever virus (YFV), Dengue virus (DENV), West Nile virus (WNV), Japanese encephalitis virus (JEV), as well as tick-borne viruses including Powassan virus (POWV) and tick-borne encephalitis virus (TBEV). Despite having been relatively obscure until the past decade, ZIKV has become a major global health concern, and is a topic of active research following multiple outbreaks across the globe. Here, we discuss ZIKV pathogenesis and the associated immunopathology, as well as advances in research, therapies, and vaccines developed using models of ZIKV pathogenesis.

Seroprevalence of human brucellosis and molecular characteristics of Brucella strains in Inner Mongolia Autonomous region of China, from 2012 to 2016

ABSTRACT In the present study, a total of 1102304 serum samples were collected to detected human brucellosis between the years 2012 and 2016 in Inner Mongolia. Overall, an average of 3.79% anti-Brucella positive in Inner Mongolia was presented but the range of positive rates were among 0.90 to 7.07% in 12 regions. Seroprevalence of human brucellosis increased gradually from 2012 to 2016. However, the incidence rate of human brucellosis showed a declining trend. One hundred and seven Brucella strains were isolated and identified as B. melitensis species, and B. melitensis biovar 3 was the predominant biovar. MLVA-11 genotypes 116 was predominant and had crucial epidemiology to the human population. All 107 strains tested were sorted into 75 MLVA-16 genotypes, with 54 single genotypes representing unique isolates. This result revealed that these Brucellosis cases had epidemiologically unrelated and sporadic characteristics. The remaining 21 shared genotypes among two to four strains, confirming the occurrence of cross-infection and multiple outbreaks. Extensive genotype-events were observed between strains from this study and Kazakhstan, Mongolia, and Turkey, these countries were key members of the grassland silk road. Long-time trade in small ruminants (sheep) in these countries has possibly promoted the spread of Brucella spp. in these regions.