Separate Outbreaks Research Articles

Public Health Applications of Patient Transfer Networks—Colorado, 2022–2023

Background: During 2021–2023, an increase in Klebsiella pneumoniae carbapenemase producing Enterobacterales species (KPC-CRE) cases occurred among patients admitted to several overlapping healthcare facilities, prompting an investigation by the Colorado Department of Public Health and Environment (CDPHE). We applied social network analysis (SNA) to identify KPC-CRE networks and other multidrug-resistant organism (MDRO) transmission, created a tool for public health prevention planning and for facilities to examine their own patient transfer connectivity, and explored additional public health and emergency preparedness applications. Methods: A statewide patient transfer network was created using 2021–2022 Medicare beneficiary data. Sub-networks were isolated from the larger network to examine a cluster of facilities involved in a KPC-CRE outbreak, defined as ≥2 KPC-CRE cases related by whole genome sequencing (WGS). WGS was conducted at the CDPHE State Lab. Highly connected facilities were determined by patient transfers between at least two KPC-CRE testing facilities. Individual patient journeys were constructed using admissions and culture date. SNA was conducted in RStudio; visualizations, network metric calculations, and clustering analysis were conducted using Gephi and ArcGIS software. Results: SNA yielded 4,864 direct patient transfers between 326 healthcare facilities (220 skilled nursing facilities, 50 acute care hospitals, 32 critical access hospitals, six long term acute care hospitals, and 18 facilities not previously classified; Figure 1). WGS identified five separate KPC-CRE outbreaks among 14 patients during February 2022–January 2023; 14 patient specimens were collected at four testing facilities. We identified five highly connected facilities in addition to the four testing facilities. Patient journeys allowed us to identify possible locations of KPC-CRE transmission in four of the five outbreaks (Figure 2). CDPHE provided guidance to all involved facilities on admission screening, routine point prevalence surveys, and interfacility communication as part of an MDRO prevention plan. CDPHE then developed the transfer network into an interactive ArcGIS dashboard enabling facilities to examine their own patient transfer patterns. Conclusions: SNA enabled CDPHE to identify at-risk facilities for KPC-CRE transmission and create an interactive tool for facility and public health use. Future applications of patient transfer networks can include geographical grouping of facilities based on transfers to zone healthcare coalitions and conduct preparedness activities, and creating medical operations preparedness plans for emergencies or disasters.

Epidemiology of sarcoptic mange in a geographically constrained insular red fox population

Background Sarcoptic mange is a skin disease caused by the contagious ectoparasite Sarcoptes scabiei, capable of suppressing and extirpating wild canid populations. Starting in 2015, we observed a multi-year epizootic of sarcoptic mange affecting a red fox (Vulpes vulpes) population on Fire Island, NY, USA. We explored the ecological factors that contributed to the spread of sarcoptic mange and characterized the epizootic in a landscape where red foxes are geographically constrained.MethodsWe tested for the presence of S. scabiei DNA in skin samples collected from deceased red foxes with lesions visibly consistent with sarcoptic mange disease. We deployed 96–100 remote trail camera stations each year to capture red fox occurrences and used generalized linear mixed-effects models to assess the affects of red fox ecology, human and other wildlife activity, and island geography on the frequency of detecting diseased red foxes. We rated the extent of visual lesions in diseased individuals and mapped the severity and variability of the sarcoptic mange disease.ResultsSkin samples that we analyzed demonstrated 99.8% similarity to S. scabiei sequences in GenBank. Our top-ranked model (weight = 0.94) showed that diseased red foxes were detected more frequently close to roadways, close to territories of other diseased red foxes, away from human shelters, and in areas with more mammal activity. There was no evidence that detection rates in humans and their dogs or distance to the nearest red fox den explained the detection rates of diseased red foxes. Although detected infrequently, we observed the most severe signs of sarcoptic mange at the periphery of residential villages. The spread of visual signs of the disease was approximately 7.3 ha/week in 2015 and 12.1 ha/week in 2017.ConclusionsWe quantified two separate outbreaks of sarcoptic mange disease that occurred > 40 km apart and were separated by a year. Sarcoptic mange revealed an unfettered spread across the red fox population. The transmission of S. scabiei mites in this system was likely driven by red fox behaviors and contact between individuals, in line with previous studies. Sarcoptic mange is likely an important contributor to red fox population dynamics within barrier island systems.Graphical

Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: transmission dynamics and epidemiological insights

BackgroundCountries across Europe have faced similar evolutions of SARS-CoV-2 variants of concern, including the Alpha, Delta, and Omicron variants.Materials and methodsWe used data from GISAID and applied a robust, automated mathematical substitution model to study the dynamics of COVID-19 variants in Europe over a period of more than 2 years, from late 2020 to early 2023. This model identifies variant substitution patterns and distinguishes between residual and dominant behavior. We used weekly sequencing data from 19 European countries to estimate the increase in transmissibility (Δβ) between consecutive SARS-CoV-2 variants. In addition, we focused on large countries with separate regional outbreaks and complex scenarios of multiple competing variants.ResultsOur model accurately reproduced the observed substitution patterns between the Alpha, Delta, and Omicron major variants. We estimated the daily variant prevalence and calculated Δβ between variants, revealing that: (i) Δβ increased progressively from the Alpha to the Omicron variant; (ii) Δβ showed a high degree of variability within Omicron variants; (iii) a higher Δβ was associated with a later emergence of the variant within a country; (iv) a higher degree of immunization of the population against previous variants was associated with a higher Δβ for the Delta variant; (v) larger countries exhibited smaller Δβ, suggesting regionally diverse outbreaks within the same country; and finally (vi) the model reliably captures the dynamics of competing variants, even in complex scenarios.ConclusionThe use of mathematical models allows for precise and reliable estimation of daily cases of each variant. By quantifying Δβ, we have tracked the spread of the different variants across Europe, highlighting a robust increase in transmissibility trend from Alpha to Omicron. Additionally, we have shown that the geographical characteristics of a country, as well as the timing of new variant entrances, can explain some of the observed differences in variant substitution dynamics across countries.

Clinical presentation and management of methanol poisoning outbreaks in Riyadh, Saudi Arabia: a retrospective analysis

BackgroundAcute methanol intoxication, whether unintentional or deliberate, necessitates prompt intervention to prevent severe morbidity and mortality. Homemade alcoholic beverages are a frequent source of such poisoning. This retrospective analysis examined two outbreaks of methanol intoxication in Saudi Arabia. It investigated the clinical presentation, implemented management strategies, and any lasting complications (sequelae) associated with these cases. The aim was to assess the potential impact of different treatment modalities and the timeliness of their initiation on patient outcomes.MethodsThis was a retrospective case series of methanol poisoning cases which presented to the adult emergency department (ED) at King Abdulaziz Medical City (KAMC) in Riyadh, Saudi Arabia. There were two separate outbreaks in the city, the first one was from September 1 to September 10, 2020 and the second one was from May 14 to May 20, 2021. Electronic charts were reviewed, and data were extracted to previously prepared data extraction sheets.ResultFrom the 22 patients who arrived in the ED alive, the most common complaints were nausea or vomiting followed by altered level of consciousness. About 9% from the patient were hypotensive, 36% were tachycardic, 41% were tachypneic and 4% were having SpO2 < 94%. Brain CT was abnormal in 6 patients. Vision impairment was the most common sequalae of methanol poisoning (7 out of 12 patients who were assessed by ophthalmologist, 58%). When the patients were divided based on severity (mild, moderate, severe), nausea or vomiting and loss of consciousness were the most common complaints among the moderate group while loss of consciousness predominated in the severe group. Two patients presented with low blood pressure and were in the sever group. The severe group had a mean Glasgow Coma Scale (GCS) of 8. Most of the patients in the severity groups underwent the same management apart from those who died or deposited. Eight patients in the severe group had to be intubated.ConclusionThis study demonstrates the multifaceted clinical presentation of methanol poisoning, culminating in a 17.4% mortality rate. Notably, our findings emphasize the critical role of prompt diagnosis and swift initiation of combined fomepizole therapy and hemodialysis in mitigating mortality and minimizing the potential for chronic visual sequelae associated with methanol poisoning.

Genomic insights into anthropozoonotic tuberculosis in captive sun bears (Helarctos malayanus) and an Asiatic black bear (Ursus thibetanus) in Cambodia

Contact between humans and wildlife presents a risk for both zoonotic and anthropozoonotic disease transmission. In this study we report the detection of human strains of Mycobacterium tuberculosis in sun bears and an Asiatic black bear in a wildlife rescue centre in Cambodia, confirming for the first time the susceptibility of these bear species to tuberculosis when in close contact with humans. After genotyping revealed two different strains of M. tuberculosis from cases occurring between 2009 and 2019, 100 isolates from 30 sun bear cases, a single Asiatic black bear case, and a human case were subjected to whole genome sequencing. We combined single nucleotide polymorphism analysis and exploration of mixed base calls with epidemiological data to indicate the evolution of each outbreak. Our results confirmed two concurrent yet separate tuberculosis outbreaks and established a likely transmission route in one outbreak where the human case acted as an intermediatory between bear cases. In both outbreaks, we observed high rates of transmission and progression to active disease, suggesting that sun bears are highly susceptible to tuberculosis if exposed under these conditions. Overall, our findings highlight the risk of bi-directional transmission of tuberculosis between humans and captive bears in high human tuberculosis burden regions, with implied considerations for veterinary and public health. We also demonstrate the use of standard genomic approaches to better understand disease outbreaks in captive wildlife settings and to inform control and prevention measures.

Taiwan ended third COVID-19 community outbreak as forecasted

Accurate forecasting of community outbreaks is crucial for governments to allocate healthcare resources correctly and implement suitable non-pharmaceutical interventions. Additionally, companies must address critical questions about stock and staff management. Society’s key concern is when businesses and organizations can resume normal operations. Between December 31st 2019 and 2021, Taiwan experienced three separate COVID-19 community outbreaks with significant time intervals in between, suggesting that each outbreak eventually came to an end. We identified the ratio of the 7-day average of local & unknown confirmed to suspected cases as the key control variable and forecasted the end of the third outbreak by the exponential model. We forecasted the end of the third outbreak on Aug. 16th with threshold ratios of 1.2·10-4\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$1.2\\cdot 10^{-4}$$\\end{document}. The real observations crossed the threshold on Aug. 27th, eleven days later than forecasted, with the last case of the third outbreak confirmed and quarantined on Sept. 20th. This demonstrated the accuracy of the proposed forecasting method in predicting the end of a local outbreak. Furthermore, we highlight that the ratio reflects the effectiveness of contact tracing. Effective contact tracing together with testing and isolation of infected individuals is crucial for ending community outbreaks.

Diagnosis, isolation and description of a novel amnoonvirus recovered from diseased fancy guppies, Poecilia reticulata.

The guppy, Poecilia reticulata, is one of the most common cultured ornamental fish species, and a popular pet fish highly desired by hobbyists worldwide due to its availability of many brilliantly coloured fish of many varieties. The susceptibility of guppies to diseases presents a remarkable concern for both breeders and hobbyists. In this study, we report the emergence of disease in fancy guppies caused by a previously uncharacterized virus in the USA. This virus was isolated from moribund guppies in two separate outbreaks in California and Alabama, from December 2021 to June 2023. The infected guppies presented with acute morbidity and mortality shortly after shipping, displaying nonspecific clinical signs and gross changes including lethargy, anorexia, swimming at the water surface, gill pallor, mild to moderate coelomic distension and occasional skin lesions including protruding scales, skin ulcers and hyperaemia. Histological changes in affected fish were mild and nonspecific; however, liver and testes from moribund fish were positive for Tilapia lake virus (TiLV), the single described member in the family Amnoonviridae, using immunohistochemistry and insitu hybridization, although the latter was weak. A virus was successfully recovered following tissue inoculation on epithelioma papulosum cyprini and snakehead fish cell lines. Whole genome sequencing and phylogenetic analyses revealed nucleotide and amino acid homologies from 78.3%-91.2%, and 78.2%-97.7%, respectively, when comparing the guppy virus genomes to TiLV isolates. Based on the criteria outlined herein, we propose the classification of this new virus, fancy tailed guppy virus (FTGV), as a member of the family Amnoonviridae, with the name Tilapinevirus poikilos (from the Greek 'poikilos', meaning of many colours; various sorts, akin to 'poecilia').

Risk factors for transmission of carbapenem-resistant Acinetobacter baumannii in outbreak situations: results of a case-control study

BackgroundAn increase in patients with multidrug-resistant organisms and associated outbreaks during the COVID-19 pandemic have been reported in various settings, including low-endemic settings. Here, we report three distinct carbapenem-resistant Acinetobacter baumannii (CRAB) outbreaks in five intensive care units of a university hospital in Berlin, Germany during the COVID-19 pandemic.MethodsA case-control study was conducted with the objective of identifying risk factors for CRAB acquisition in outbreak situations. Data utilized for the case-control study came from the investigation of three separate CRAB outbreaks during the COVID-19 pandemic (August 2020– March 2021). Cases were defined as outbreak patients with hospital-acquired CRAB. Controls did not have any CRAB positive microbiological findings and were hospitalized at the same ward and for a similar duration as the respective case. Control patients were matched retrospectively in a 2:1 ratio. Parameters routinely collected in the context of outbreak management and data obtained retrospectively specifically for the case-control study were included in the analysis. To analyze risk factors for CRAB acquisition, univariable and multivariable analyses to calculate odds ratios (OR) and 95% confidence intervals (CI) were performed using a conditional logistic regression model.ResultsThe outbreaks contained 26 cases with hospital-acquired CRAB in five different intensive care units. Two exposures were identified to be independent risk factors for nosocomial CRAB acquisition by the multivariable regression analysis: Sharing a patient room with a CRAB patient before availability of the microbiological result was associated with a more than tenfold increase in the risk of nosocomial CRAB acquisition (OR: 10.7, CI: 2.3–50.9), while undergoing bronchoscopy increased the risk more than six times (OR: 6.9, CI: 1.3–38.1).ConclusionsThe risk factors identified, sharing a patient room with a CRAB patient and undergoing bronchoscopy, could point to an underperformance of basic infection control measure, particularly hand hygiene compliance and handling of medical devices. Both findings reinforce the need for continued promotion of infection control measures. Given that the outbreaks occurred in the first year of the COVID-19 pandemic, our study serves as a reminder that a heightened focus on airborne precautions should not lead to a neglect of other transmission-based precautions.

Global emergence of a hypervirulent carbapenem-resistant Escherichia coli ST410 clone

Carbapenem-resistant Escherichia coli (CREC) ST410 has recently emerged as a major global health problem. Here, we report a shift in CREC prevalence in Chinese hospitals between 2017 and 2021 with ST410 becoming the most commonly isolated sequence type. Genomic analysis identifies a hypervirulent CREC ST410 clone, B5/H24RxC, which caused two separate outbreaks in a children’s hospital. It may have emerged from the previously characterised B4/H24RxC in 2006 and has been isolated in ten other countries from 2015 to 2021. Compared with B4/H24RxC, B5/H24RxC lacks the blaOXA-181-bearing X3 plasmid, but carries a F-type plasmid containing blaNDM-5. Most of B5/H24RxC also carry a high pathogenicity island and a novel O-antigen gene cluster. We find that B5/H24RxC grew faster in vitro and is more virulent in vivo. The identification of this newly emerged but already globally disseminated hypervirulent CREC clone, highlights the ongoing evolution of ST410 towards increased resistance and virulence.

First report of natural Cyprinid herpesvirus-2 infection associated with fatal outbreaks of goldfish (Carassius auratus) farms in Thailand

Two separate fatal outbreaks occurred in ornamental goldfish (Carassius auratus) farms, marked by clinical signs including depression, scale protrusion, massive mucus production, and mortality rates exceeding 50% were identified in Thailand. Detailed histological examination revealed extensive necrosis of hematopoietic tissues in kidneys and spleen, together with marked necrotizing branchitis and brachium hyperplasia. Furthermore, characteristic intranuclear inclusion bodies with margination of chromatin were observed in hematopoietic cells in the spleen and kidneys, and in gill epithelial cells. Conventional polymerase chain reaction (PCR) detected Cyprinid herpesvirus-2 (CyHV-2) DNA in the affected populations, with no presence of CyHV-1 or CyHV-3 DNA. Using quantitative PCR (qPCR), we found that viral DNA largely localized within the spleen and kidneys, followed by gills, heart, brain, and liver. In situ hybridization demonstrated CyHV-2 tropism, with localization identified in hematopoietic cells in the kidney and spleen, and in epithelial cells in the gill lamellae and skin. Apart from hematopoietic cells in kidneys and spleen, transmission electron microscopy confirmed herpesviral particles within the epithelial cells in the gills and skin of infected fish. Genomic analysis was conducted on partial genome sequences of CyHV-2 DNA polymerase and helicase genes, and the tandem repeats region were obtained and subsequently characterized using next generation sequencing-based approach. This data suggested that these two CyHV-2 Thai strains were nearly identical and closely related to other CyHV-2 strains found in Asia. Genomic analysis based on the helicase gene revealed that the CyHV-2 Thai strains were unique and distinct by creating monophyletic clade. Our findings report the first identification of CyHV-2 in Thailand for first time, and highlight its potential pathological implications. While these Thai sequences of CyHV-2 are indeed unique, further investigations are in progress to confirm the definitive role of this genetic variability in relation to its virulence.

Phylogeography and host specificity of Pasteurellaceae pathogenic to sea-farmed fish in the north-east Atlantic.

The present study was undertaken to address the recent spate of pasteurellosis outbreaks among sea-farmed Atlantic salmon (Salmo salar) in Norway and Scotland, coinciding with sporadic disease episodes in lumpfish (Cyclopterus lumpus) used for delousing purposes in salmon farms. Genome assemblies from 86 bacterial isolates cultured from diseased salmon or lumpfish confirmed them all as bona fide members of the Pasteurellaceae family, with phylogenetic reconstruction dividing them into two distinct branches sharing <88% average nucleotide identity. These branches therefore constitute two separate species, namely Pasteurella skyensis and the as-yet invalidly named "Pasteurella atlantica". Both species further stratify into multiple discrete genomovars (gv.) and/or lineages, each being nearly or fully exclusive to a particular host, geographic region, and/or time period. Pasteurellosis in lumpfish is, irrespective of spatiotemporal origin, linked almost exclusively to the highly conserved "P. atlantica gv. cyclopteri" (Pac). In contrast, pasteurellosis in Norwegian sea-farmed salmon, dominated since the late-1980s by "P. atlantica gv. salmonicida" (Pas), first saw three specific lineages (Pas-1, -2, and -3) causing separate, geographically restricted, and short-lived outbreaks, before a fourth (Pas-4) emerged recently and became more widely disseminated. A similar situation involving P. skyensis (Ps) has apparently been unfolding in Scottish salmon farming since the mid-1990s, where two historic (Ps-1 and -2) and one contemporary (Ps-3) lineages have been recorded. While the epidemiology underlying all these outbreaks/epizootics remains unclear, repeated detection of 16S rRNA gene amplicons very closely related to P. skyensis and "P. atlantica" from at least five cetacean species worldwide raises the question as to whether marine mammals may play a part, possibly as reservoirs. In fact, the close relationship between the studied isolates and Phocoenobacter uteri associated with harbor porpoise (Phocoena phocoena), and their relatively distant relationship with other members of the genus Pasteurella, suggests that both P. skyensis and "P. atlantica" should be moved to the genus Phocoenobacter.

Bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting.

Most current Salmonella subtyping analyses rely on whole genome sequencing (WGS), which focuses on the high-resolution analysis of single genomes or multiple single genomes from the isolated colonies on microbiological agar plates. In this study, we introduce bioinformatics innovations for a metagenomic outbreak response workflow that accurately identifies multiple Salmonella serovars at the same time. bettercallsal is one of the first analysis tools to identify multiple Salmonella enterica serotypes from metagenomic or quasi-metagenomic datasets with high accuracy, allowing these isolate-independent methods to be incorporated into surveillance and root cause investigations. It was tested on an in silico benchmark dataset comprising 29 unique Salmonella serovars, 46 non-Salmonella bacterial genomes, and 10 viral genomes at varying read depths and on previously well-characterized and sequenced non-selective primary and selective enrichments of papaya and peach samples from separate outbreak investigations that resulted in the identification of multiple Salmonella serovars using traditional isolate culturing and WGS as well as nucleic acid assays. Analyses were also conducted on these datasets using a custom-built k-mer tool, SeqSero2, and Kallisto to compare serotype calling to bettercallsal. The in silico dataset analyzed with bettercallsal achieved the maximum precision, recall, and accuracy of 100, 83, and 94%, respectively. In the papaya outbreak samples, bettercallsal identified the presence of multiple serovars in agreement with the Luminex® xMAP assay results and also identified more serovars per sample, as evidenced by NCBI SNP clustering. In peach outbreak samples, bettercallsal identified two serovars in concordance with k-mer analysis and the Luminex xMAP assay. The genome hit reported by bettercallsal clustered with the chicken isolate genome, as reported by the FDA peach outbreak investigation from sequenced isolates (WGS). Overall, bettercallsal outperformed k-mer, Seqsero2, and Kallisto in identifying multiple serovars from enrichment cultures using shotgun metagenomic sequencing.

Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

Whole genome sequencing of SARS-CoV-2 has occurred at an unprecedented scale, and can be exploited for characterising outbreak risks at the fine-scale needed to inform control strategies. One setting at continued risk of COVID-19 outbreaks are higher education institutions, associated with student movements at the start of term, close living conditions within residential halls, and high social contact rates. Here we analysed SARS-CoV-2 whole genome sequences in combination with epidemiological data to investigate a large cluster of student cases associated with University of Glasgow accommodation in autumn 2020, Scotland. We identified 519 student cases of SARS-CoV-2 infection associated with this large cluster through contact tracing data, with 30% sequencing coverage for further analysis. We estimated at least 11 independent introductions of SARS-CoV-2 into the student population, with four comprising the majority of detected cases and consistent with separate outbreaks. These four outbreaks were curtailed within a week following implementation of control measures. The impact of student infections on the local community was short-term despite an underlying increase in community infections. Our study highlights the need for context-specific information in the formation of public health policy for higher educational settings.

Salmonella enterica serovar Brandenburg abortions in dairy cattle.

Two separate late-term abortion outbreaks in Jersey heifers in July 2020 and December 2020 were investigated by the Iowa State University Veterinary Diagnostic Laboratory. We evaluated 3 whole fetuses and 11 sets of fresh and formalin-fixed fetal tissues during the course of the outbreaks. The late-term abortions were first identified at a heifer development site and subsequently observed at the dairy farm. Aborted fetuses had moderate-to-marked postmortem autolysis with no gross lesions identified. Observed clinical signs in cows at the dairy farm ranged from intermittent loose stools to acute post-abortion pyrexia and reduced feed intake. Routine histopathology and reproductive bacterial culture revealed acute, suppurative placentitis with moderate-to-heavy growth of Salmonella spp. group B from stomach contents, liver, placenta, and heifer fecal contents. Serotyping identified Salmonella enterica subsp. enterica serovar Brandenburg in all 14 fresh tissue cases, as well as individual and pooled heifer feces. Whole-genome sequencing analysis revealed that all isolates belonged to ST type 873 and possessed typhoid toxin genes, several fimbrial gene clusters, type III secretion system genes, and several pathogenicity islands. Abortions caused by Salmonella Brandenburg have not been reported previously in dairy cattle in the United States, to our knowledge.

The Kivu Ebola epidemic

The Kivu Ebola epidemic[note 1] began on 1 August 2018, when four cases of Ebola virus disease (EVD) were confirmed in the eastern region of Kivu in the Democratic Republic of the Congo (DRC).[2][3][4] The disease affected the DRC, Uganda, and is suspected to have also affected Tanzania, though the Ministry of Health there never shared information with the WHO.[5] The outbreak was declared ended on 25 June 2020, with a total of 3,470 cases and 2,280 deaths.[6][7] Other locations in the DRC affected included the Ituri Province, where the first case was confirmed on 13 August 2018.[1] In November 2018, it became the biggest Ebola outbreak in the DRC's history,[8][9][10] and by November, it had become the second-largest Ebola outbreak in recorded history,[11][12] behind only the 2013–2016 Western Africa epidemic. On 3 May 2019, 9 months into the outbreak, the DRC death toll surpassed 1,000.[13][14] In June 2019, the virus reached Uganda, having infected a 5-year-old Congolese boy who entered with his family,[15] but this was contained. Since January 2015, the affected province and general area have been experiencing a military conflict, which hindered treatment and prevention efforts. The World Health Organization (WHO) has described the combination of military conflict and civilian distress as a potential "perfect storm" that could lead to a rapid worsening of the situation.[16][17] In May 2019, the WHO reported that, since January of that year, there had been 42 attacks on health facilities and 85 health workers had been wounded or killed. In some areas, aid organizations have had to stop their work due to violence.[18] Health workers also had to deal with misinformation spread by opposing politicians.[19] Due to the deteriorating security situation in North Kivu and surrounding areas, the WHO raised the risk assessment at the national and regional level from "high" to "very high" in September 2018.[20] In October, the United Nations Security Council stressed that all armed hostility in the DRC should come to a stop to address the ongoing outbreak better.[21][22][23] A confirmed case in Goma triggered the decision by the WHO to convene an emergency committee for the fourth time,[24][25] and on 17 July 2019, the WHO announced a Public Health Emergency of International Concern (PHEIC), the highest level of alarm the WHO can sound.[26] On 15 September 2019, some slowdown of cases was noted in the DRC.[27] However, contact tracing continued to be less than 100%; at the time, it was at 89%.[27] In mid-October the transmission of the virus had significantly reduced; by then it was confined to the Mandima region near where the outbreak began, and was only affecting 27 health zones in the DRC (down from a peak of 207).[28] New cases decreased to zero by 17 February 2020,[29] but after 52 days without a case, surveillance and response teams confirmed three new cases in mid-April.[30][31][32] As a new and separate outbreak, was reported on 1 June 2020 in Équateur Province in north-western DRC, described as the eleventh Ebola outbreak since records began;[33] after almost two years the tenth outbreak was declared ended on 25 June 2020, with a total of 3,470 cases and 2,280 deaths.[34][7]

Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California

BackgroundDuring the COVID-19 pandemic within the United States, much of the responsibility for diagnostic testing and epidemiologic response has relied on the action of county-level departments of public health. Here we describe the integration of genomic surveillance into epidemiologic response within Humboldt County, a rural county in northwest California.MethodsThrough a collaborative effort, 853 whole SARS-CoV-2 genomes were generated, representing ~58% of the 1,449 SARS-CoV-2-positive cases detected in Humboldt County as of March 12, 2021. Phylogenetic analysis of these data was used to develop a comprehensive understanding of SARS-CoV-2 introductions to the county and to support contact tracing and epidemiologic investigations of all large outbreaks in the county.ResultsIn the case of an outbreak on a commercial farm, viral genomic data were used to validate reported epidemiologic links and link additional cases within the community who did not report a farm exposure to the outbreak. During a separate outbreak within a skilled nursing facility, genomic surveillance data were used to rule out the putative index case, detect the emergence of an independent Spike:N501Y substitution, and verify that the outbreak had been brought under control.ConclusionsThese use cases demonstrate how developing genomic surveillance capacity within local public health departments can support timely and responsive deployment of genomic epidemiology for surveillance and outbreak response based on local needs and priorities.

The Kivu Ebola Epidemic

The Kivu Ebola epidemic began on 1 August 2018, when four cases of Ebola virus disease (EVD) were confirmed in the eastern region of Kivu in the Democratic Republic of the Congo (DRC). The disease affected the DRC, Uganda, and is suspected to have also affected Tanzania, though the Ministry of Health there never shared information with the WHO. The outbreak was declared ended on 25 June 2020, with a total of 3,470 cases and 2,280 deaths. Other locations in the DRC affected included the Ituri Province, where the first case was confirmed on 13 August 2018. In November 2018, it became the biggest Ebola outbreak in the DRC's history, and by November, it had become the second-largest Ebola outbreak in recorded history, behind only the 2013–2016 Western Africa epidemic. On 3 May 2019, 9 months into the outbreak, the DRC death toll surpassed 1,000. In June 2019, the virus reached Uganda, having infected a 5-year-old Congolese boy who entered with his family, but this was contained. Since January 2015, the affected province and general area have been experiencing a military conflict, which hindered treatment and prevention efforts. The World Health Organization (WHO) has described the combination of military conflict and civilian distress as a potential "perfect storm" that could lead to a rapid worsening of the situation. In May 2019, the WHO reported that, since January of that year, there had been 42 attacks on health facilities and 85 health workers had been wounded or killed. In some areas, aid organizations have had to stop their work due to violence. Health workers also had to deal with misinformation spread by opposing politicians. Due to the deteriorating security situation in North Kivu and surrounding areas, the WHO raised the risk assessment at the national and regional level from "high" to "very high" in September 2018. In October, the United Nations Security Council stressed that all armed hostility in the DRC should come to a stop to address the ongoing outbreak better. A confirmed case in Goma triggered the decision by the WHO to convene an emergency committee for the fourth time, and on 17 July 2019, the WHO announced a Public Health Emergency of International Concern (PHEIC), the highest level of alarm the WHO can sound. On 15 September 2019, some slowdown of cases was noted in the DRC. However, contact tracing continued to be less than 100%; at the time, it was at 89%. In mid-October the transmission of the virus had significantly reduced; by then it was confined to the Mandima region near where the outbreak began, and was only affecting 27 health zones in the DRC (down from a peak of 207). New cases decreased to zero by 17 February 2020, but after 52 days without a case, surveillance and response teams confirmed three new cases in mid-April. As a new and separate outbreak, was reported on 1 June 2020 in Équateur Province in north-western DRC, described as the eleventh Ebola outbreak since records began; after almost two years the tenth outbreak was declared ended on 25 June 2020, with a total of 3,470 cases and 2,280 deaths.

A Series of Papaya-Associated Salmonella Illness Outbreak Investigations in 2017 and 2019: A Focus on Traceback, Laboratory, and Collaborative Efforts

In 2017 and 2019, five outbreaks of infections from multiple strains of Salmonella linked to the consumption of whole, fresh Maradol papayas were reported in the United States, resulting in 325 ill persons. Traceback, laboratory, and epidemiologic evidence indicated papayas as the likely vehicle for each of these outbreaks and identified the source of papayas. State and U.S. Food and Drug Administration (FDA) laboratories recovered Salmonella from papaya samples from various points of distribution, including at import entry, and conducted serotyping, pulsed-field gel electrophoresis, and phylogenetic analyses of whole genome sequencing data. Federal and state partners led traceback investigations to determine the source of papayas. Four different suppliers of papayas were linked by traceback and laboratory results to five separate outbreaks of Salmonella infections associated with papayas. In 2017, multiple states tested papaya samples collected at retail, and Maryland and Virginia investigators recovered strains of Salmonella associated with one outbreak. FDA collected 183 papaya samples in 2017, and 11 samples yielded 62 isolates of Salmonella. Eleven serotypes of Salmonella were recovered from FDA papaya samples, and nine serotypes were closely related genetically by pulsed-field gel electrophoresis and whole genome sequencing to clinical isolates of four outbreaks, including the outbreak associated with positive state sample results. Four farms in Mexico were identified, and their names were released to the general public, retailers, and foreign authorities. In 2019, FDA collected 119 papaya samples, three of which yielded Salmonella; none yielded the 2019 outbreak strain. Investigators determined that papayas of interest had been sourced from a single farm in Campeche, Mexico, through traceback. This information was used to protect public health through public guidance, recalls, and import alerts and helped FDA collaborate with Mexican regulatory partners to enhance the food safety requirements for papayas imported from Mexico.

Complete Genome Sequences of Three Clinical Listeria monocytogenes Sequence Type 8 Strains from Recent German Listeriosis Outbreaks.

We report here the closed genome sequences of three clinical Listeria monocytogenes strains of multilocus sequence typing (MLST) sequence type 8 (ST8). These strains are representatives of three separate listeriosis outbreak clusters (Alpha1, Pi4, and Sigma1) that affected Germany between 2012 and 2020.

Sequential detection framework for real-time biosurveillance based on Shiryaev-Roberts procedure with illustrations using COVID-19 incidence data

This article develops a detection framework using Bayesian philosophy by adaptation of Shiryaev's and Roberts' methodology. We propose two unifying versions directly applicable in industrial process control and easily extendable to public health infectious disease surveillance via some data detrending and/or demodulation. The root idea uses the sum of likelihood ratios upon which an optimal stopping criterion is based. It sets a prior on the epoch of a change, allows the flexibility to elicit a prior distribution on other process parameters, and attempts to minimize an expected loss function. A sensitivity analysis is conducted for validation and performance assessment and analytical formulas are derived. The methods are successfully applied to the European Union Centre for Disease Control (ECDC) open-source global COVID-19 incidence data. We further lay out scenarios where interest may switch to the detection of separate outbreaks with similar syndromes during an already evolving epidemic. We view our approach as a toolkit with a potential to augment early reports to sentinels in syndromic surveillance and in biosurveillance.