The French human Salmonella surveillance system: evaluation of timeliness of laboratory reporting and factors associated with delays, 2007 to 2011

Lessons Learned From Implementation of Mpox Surveillance During an Outbreak Response in Tennessee, 2022

OBJECTIVES

Mpox surveillance was integral during the 2022 outbreak response. We evaluated implementation of mpox surveillance in Tennessee during an outbreak response and made recommendations for surveillance during emerging infectious disease outbreaks.

METHODS

To understand surveillance implementation, system processes, and areas for improvement, we conducted 8 semistructured focus groups and 7 interviews with 36 health care, laboratory, and health department representatives during September 9-20, 2022. We categorized and analyzed session transcription and notes. We analyzed completeness and timeliness of surveillance data, including 349 orthopoxvirus-positive laboratory reports from commercial, public health, and health system laboratories during July 1-August 31, 2022.

RESULTS

Participants described an evolving system and noted that existing informatics platforms inefficiently supported iterations of reporting requirements. Clear communication, standardization of terminology, and shared, adaptable, and user-friendly informatics platforms were prioritized for future emerging infectious disease surveillance systems. Laboratory-reported epidemiologic information was often incomplete; only 55% (191 of 349) of reports included patient address and telephone number. The median time from symptom onset to specimen collection was 5 days (IQR, 3-6 d), from specimen collection to laboratory reporting was 3 days (IQR, 1-4 d), from laboratory reporting to patient interview was 1 day (IQR, 1-3 d), and from symptom onset to patient interview was 9 days (IQR, 7-12 d).

CONCLUSIONS

Future emerging infectious disease responses would benefit from standardized surveillance approaches that facilitate rapid implementation. Closer collaboration among informatics, laboratory, and clinical partners across jurisdictions and agencies in determining system priorities and designing workflow processes could improve flexibility of the surveillance platform and completeness and timeliness of laboratory reporting. Improved timeliness will facilitate public health response and intervention, thereby mitigating morbidity.

The perspectives of biomarker-based electrochemical immunosensors, artificial intelligence and the Internet of Medical Things toward COVID-19 diagnosis and management

The World Health Organization (WHO) has declared the COVID-19 an international health emergency due to the severity of infection progression, which became more severe due to its continuous spread globally and the unavailability of appropriate therapy and diagnostics systems. Thus, there is a need for efficient devices to detect SARS-CoV-2 infection at an early stage. Nowadays, the reverse transcription polymerase chain reaction (RT-PCR) technique is being applied for detecting this virus around the globe; however, factors such as stringent expertise, long diagnostic times, invasive and painful screening, and high costs have restricted the use of RT-PCR methods for rapid diagnostics. Therefore, the development of cost-effective, portable, sensitive, prompt and selective sensing systems to detect SARS-CoV-2 in biofluids at fM/pM/nM concentrations would be a breakthrough in diagnostics. Immunosensors that show increased specificity and sensitivity are considerably fast and do not imply costly reagents or instruments, reducing the cost for COVID-19 detection. The current developments in immunosensors perhaps signify the most significant opportunity for a rapid assay to detect COVID-19, without the need of highly skilled professionals and specialized tools to interpret results. Artificial intelligence (AI) and the Internet of Medical Things (IoMT) can also be equipped with this immunosensing approach to investigate useful networking through database management, sharing, and analytics to prevent and manage COVID-19. Herein, we represent the collective concepts of biomarker-based immunosensors along with AI and IoMT as smart sensing strategies with bioinformatics approach to monitor non-invasive early stage SARS-CoV-2 development, with fast point-of-care (POC) diagnostics as the crucial goal. This approach should be implemented quickly and verified practicality for clinical samples before being set in the present times for mass-diagnostic research.

Quality and Utility of Information Captured by Surveillance Systems Relevant to Antimicrobial Resistance (AMR): A Systematic Review

Health surveillance systems are considered vital for combatting antimicrobial resistance (AMR); however, the evidence-base on the effectiveness of these systems in providing information that can be used by healthcare professionals, or the acceptability of these systems by users, has not been reviewed. A systematic review was conducted of a number of databases to synthesise the evidence. The review identified 43 studies that met the inclusion criteria, conducted in 18 countries and used 11 attributes in their assessment of surveillance systems. The majority of systems evaluated were for monitoring the incidence of tuberculosis. The studies found that most surveillance systems were underperforming in key attributes that relate to both effectiveness and acceptability. We identified that two features of systems (ease of use and users' awareness of systems) were associated with greater acceptability and completeness of systems. We recommend prioritising these for the improvement of existing systems, as well as ensuring consistency in the definition of attributes studied, to allow a more consistent approach in evaluations of surveillance systems, and to facilitate the identification of the attributes that have the greatest impact on the utility of data produced.

Comprehensive Review on Current Interventions, Diagnostics, and Nanotechnology Perspectives against SARS-CoV-2

The coronavirus disease 2019 (COVID-19) has dramatically challenged the healthcare system of almost all countries. The authorities are struggling to minimize the mortality along with ameliorating the economic downturn. Unfortunately, until now, there has been no promising medicine or vaccine available. Herein, we deliver perspectives of nanotechnology for increasing the specificity and sensitivity of current interventional platforms toward the urgent need of quickly deployable solutions. This review summarizes the recent involvement of nanotechnology from the development of a biosensor to fabrication of a multifunctional nanohybrid system for respiratory and deadly viruses, along with the recent interventions and current understanding about severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.

Disentangling a complex nationwide Salmonella Dublin outbreak associated with raw-milk cheese consumption, France, 2015 to 2016

On 18 January 2016, the French National Reference Centre for Salmonella reported to Santé publique France an excess of Salmonella enterica serotype Dublin (S. Dublin) infections. We investigated to identify the source of infection and implement control measures. Whole genome sequencing (WGS) and multilocus variable-number tandem repeat analysis (MLVA) were performed to identify microbiological clusters and links among cases, animal and food sources. Clusters were defined as isolates with less than 15 single nucleotide polymorphisms determined by WGS and/or with identical MLVA pattern. We compared different clusters of cases with other cases (case–case study) and controls recruited from a web-based cohort (case–control study) in terms of food consumption. We interviewed 63/83 (76%) cases; 2,914 controls completed a questionnaire. Both studies’ findings indicated that successive S. Dublin outbreaks from different sources had occurred between November 2015 and March 2016. In the case–control study, cases of distinct WGS clusters were more likely to have consumed Morbier (adjusted odds ratio (aOR): 14; 95% confidence interval (CI): 4.8–42) or Vacherin Mont d’Or (aOR: 27; 95% CI: 6.8–105), two bovine raw-milk cheeses. Based on these results, the Ministry of Agriculture launched a reinforced control plan for processing plants of raw-milk cheeses in the production region, to prevent future outbreaks.

COVID-19 Infection Diagnosis: Potential Impact of Isothermal Amplification Technology to Reduce Community Transmission of SARS-CoV-2

The current coronavirus disease 2019 (COVID-19) pandemic is largely driven by community transmission, after 2019 novel Coronavirus (2019-nCoV or SARS-CoV-2) crosses the borders. To stop the spread, rapid testing is required at community clinics and hospitals. These rapid tests should be comparable with the standard PCR technology. Isothermal amplification technology provides an excellent alternative that is highly amenable to resource limited settings, where expertise and infrastructure to support PCR are not available. In this review, we provide a brief description of isothermal amplification technology, its potential and the gaps that need to be considered for SARS-CoV-2 detection. Among this emerging technology, loop-mediated amplification (LAMP), recombinase polymerase amplification (RPA) and Nicking enzyme-assisted reaction (NEAR) technologies have been identified as potential platforms that could be implemented at community level, without samples referral to a centralized laboratory and prolonged turnaround time associated with the standard COVID-19 RT-PCR test. LAMP, for example, has recently been shown to be comparable with PCR and could be performed in less than 30 min by non-laboratory staff, without RNA extractions commonly associated with PCR. Interestingly, NEAR (ID NOW™ COVID-19 (Abbott, IL, USA) was able to detect the virus in 5 min. More so, isothermal platforms are cost effective and could easily be scaled up to resource limited settings. Diagnostics developers, scientific community and commercial companies could consider this alternative method to help stop the spread of COVID-19.

2019 Novel Coronavirus Disease (COVID-19): Paving the Road for Rapid Detection and Point-of-Care Diagnostics

We believe a point-of-care (PoC) device for the rapid detection of the 2019 novel Coronavirus (SARS-CoV-2) is crucial and urgently needed. With this perspective, we give suggestions regarding a potential candidate for the rapid detection of the coronavirus disease 2019 (COVID-19), as well as factors for the preparedness and response to the outbreak of the COVID-19.

Evaluating Response Time in Zanzibar's Malaria Elimination Case-Based Surveillance-Response System

As countries transition toward malaria elimination, malaria programs rely on surveillance-response systems, which are often supported by web- and mobile phone-based reporting tools. Such surveillance-response systems are interventions for elimination, making it important to determine if they are operating optimally. A metric to measure this by is timeliness. This study used a mixed-methods approach to investigate the response time of Zanzibar's malaria elimination surveillance-response system, Malaria Case Notification (MCN). MCN conducts both passive and reactive case detection, supported by a mobile phone-based reporting tool called Coconut Surveillance. Using data obtained from RTI International and the Zanzibar Malaria Elimination Program (ZAMEP), analysis of summary statistics was conducted to investigate the association of response time with geography, and time series techniques were used to investigate trends in response time and its association with the number of reported cases. Results indicated that response time varied by the district in Zanzibar (0.6-6.05 days) and that it was not associated with calendar time or the number of reported cases. Survey responses and focus groups with a cadre of health workers, district malaria surveillance officers, shed light on operational challenges faced during case investigation, such as incomplete health records and transportation issues, which stem from deficiencies in aspects of ZAMEP's program management. These findings illustrate that timely response for malaria elimination depends on effective program management, despite the automation of web-based or mobile phone-based tools. For surveillance-response systems to work optimally, malaria programs should ensure that optimal management practices are in place.

Timeliness in the German surveillance system for infectious diseases: Amendment of the infection protection act in 2013 decreased local reporting time to 1 day

Time needed to report surveillance data within the public health service delays public health actions. The amendment to the infection protection act (IfSG) from 29 March 2013 requires local and state public health agencies to report surveillance data within one working day instead of one week. We analysed factors associated with reporting time and evaluated the IfSG amendment. Local reporting time is the time between date of notification and date of export to the state public health agency and state reporting time is time between date of arrival at the state public health agency and the date of export. We selected cases reported between 28 March 2012 and 28 March 2014. We calculated the median local and state reporting time, stratified by potentially influential factors, computed a negative binominal regression model and assessed quality and workload parameters. Before the IfSG amendment the median local reporting time was 4 days and 1 day afterwards. The state reporting time was 0 days before and after. Influential factors are the individual local public health agency, the notified disease, the notification software and the day of the week. Data quality and workload parameters did not change. The IfSG amendment has decreased local reporting time, no relevant loss of data quality or identifiable workload-increase could be detected. State reporting time is negligible. We recommend efforts to harmonise practices of local public health agencies including the exclusive use of software with fully compatible interfaces.

Timeliness of Measles Laboratory Reporting and Factors Associated with Delays, Zhejiang Province, China, 2009-2015

In 2006, China targeted measles for elimination by 2012, but the goal was not achieved. In line with this goal, the timeliness of measles laboratory reporting should be evaluated to improve efficiency in implementing control measures. Laboratory-confirmed suspected measles cases reported to the measles surveillance system in Zhejiang Province, China, from 2009 to 2015 were collected. Three reporting periods were defined: transport duration (period from serum collected to serum received in lab), analysis duration (period from serum received to the result being reported), and total reporting duration. The median was calculated for each period. Associations between total reporting delay and other factors were accessed using logistic regression model. A total of 18,518 laboratory-confirmed suspected measles cases were collected. For transport duration, the median was within 1 day, and no variation was observed among different years. For analysis duration, the median decreased from 3 days in 2009 to 1 day in 2015. For total reporting duration, the median decreased from 5 days in 2009 to 2 days in 2015. The median of total delay was 13 days during the 7 years. The proportion of cases notified within the time limit was found to increase, indicating a tendency toward more efficient laboratory reporting. Moreover, timeliness was influenced by various external factors: reporting from CDC, reporting from counties with higher economic status, and reporting in spring were the variables associated with shorter delays. Timeliness of measles laboratory reporting has increased annually in China. Health administration departments need to pay more attention to measles laboratory surveillance in counties with lower economic status.

Evaluating the Timeliness of Enteric Disease Surveillance in British Columbia, Canada, 2012-13

Timely surveillance of enteric diseases is necessary to identify and control cases and outbreaks. Our objective was to evaluate the timeliness of enteric disease surveillance in British Columbia, Canada, compare these results to other settings, and recommend improvements. In 2012 and 2013, information was collected from case report forms and laboratory information systems on 2615 Salmonella, shigatoxin-producing E. coli, Shigella, and Listeria infections. Twelve date variables representing the surveillance process from onset of symptoms to case interview and final laboratory results were collected, and intervals were measured. The median time from onset of symptoms to reporting subtyping results to BC epidemiologists was 26-36 days and from onset of symptoms to case interview was 12-14 days. Our findings were comparable to the international literature except for a longer time (up to 29 day difference) to reporting of PFGE results to epidemiologists in BC. Such a delay may impact our ability to identify and solve outbreaks. Several process and system changes were implemented which should improve the timeliness of enteric disease surveillance.

Evaluating the timeliness of reporting in a First Nations communicable diseases program

Background

Timely reporting of communicable diseases is necessary to enable a prompt response to mitigate and control outbreaks. This is especially true among First Nations communities due to a number of factors, including unique social determinants of health, which can contribute to rapid disease transmission.

Objective

To assess the timeliness of reporting for 12 notifiable communicable diseases in the Northern Inter-Tribal Health Authority, which includes 33 First Nations on-reserve communities in Northern Saskatchewan, Canada, and to assess whether there were differences in reporting times depending on degree of remoteness of community, season or year.

Methods

Data for four sexually transmitted infections (STIs) and eight other communicable diseases were abstracted from the integrated Public Health Information System (iPHIS) between 2008 and 2013 and compared against the targets set for reporting in the Saskatchewan Communicable Disease Control Manual. The reporting time was defined as the duration from client exposure or presentation at clinic to the case notification day at Saskatchewan's Ministry of Health. Communicable diseases were evaluated for proportion of cases reported within recommended time, and mean reporting time. Geographical and reporting data were also recorded to assess variations in reporting time among different northern communities and according to season or year.

Results

A total of 9,767 records were identified for the 12 diseases; all had a 14-day recommended reporting time, with the exception of shigellosis, which had a three-day reporting time. Overall, 93.6% of the diseases were reported in the recommended reporting time, although there was variability among the diseases. All four of the STIs (chlamydia, gonococcal infections, HIV and syphilis) had over 90% of cases reported within the 14-day recommended time period. Other communicable diseases reporting times varied from a high of 93.4% for methicillin-resistant Staphylococcus aureus (MRSA), 91.7% for lab-confirmed influenza and 89.1% for streptococcal A-invasive disease to a low of 16.2% for shigellosis and 12.2% for pertussis. Salmonellosis and pneumococcal-invasive disease were intermediary with 77.4% and 72.2%, respectively. Mean reporting times indicated that eight of the 12 diseases (66.7%) had reporting times similar to or better than recommended times. There appeared to be a correlation between longer reporting periods and the more northern communities. There were no seasonal variations found but yearly-trend analysis demonstrated an anomalous year in 2011, in which all communicable diseases with the exception of STIs experienced a peak in reporting delays.

Conclusion

Overall, communicable disease reporting in this northern health authority program met recommended reporting times, although there were variations according to the disease, the area reporting and the year. Further research is needed to understand these variations in order to inform efforts to strengthen communicable disease surveillance among First Nations communities.

Value of evidence from syndromic surveillance with cumulative evidence from multiple data streams with delayed reporting

Delayed reporting of health data may hamper the early detection of infectious diseases in surveillance systems. Furthermore, combining multiple data streams, e.g. aiming at improving a system's sensitivity, can be challenging. In this study, we used a Bayesian framework where the result is presented as the value of evidence, i.e. the likelihood ratio for the evidence under outbreak versus baseline conditions. Based on a historical data set of routinely collected cattle mortality events, we evaluated outbreak detection performance (sensitivity, time to detection, in-control run length) under the Bayesian approach among three scenarios: presence of delayed data reporting, but not accounting for it; presence of delayed data reporting accounted for; and absence of delayed data reporting (i.e. an ideal system). Performance on larger and smaller outbreaks was compared with a classical approach, considering syndromes separately or combined. We found that the Bayesian approach performed better than the classical approach, especially for the smaller outbreaks. Furthermore, the Bayesian approach performed similarly well in the scenario where delayed reporting was accounted for to the scenario where it was absent. We argue that the value of evidence framework may be suitable for surveillance systems with multiple syndromes and delayed reporting of data.

Multinational outbreak of travel-related Salmonella Chester infections in Europe, summers 2014 and 2015

Between 2014 and 2015, the European Centre for Disease Prevention and Control was informed of an increase in numbers of Salmonella enterica serotype Chester cases with travel to Morocco occurring in six European countries. Epidemiological and microbiological investigations were conducted. In addition to gathering information on the characteristics of cases from the different countries in 2014, the epidemiological investigation comprised a matched case-case study involving French patients with salmonellosis who travelled to Morocco that year. A univariate conditional logistic regression was performed to quantify associations. The microbiological study included a whole genome sequencing (WGS) analysis of clinical and non-human isolates of S. Chester of varied place and year of isolation. A total of 162 cases, mostly from France, followed by Belgium, the Netherlands, Spain, Denmark and Sweden were reported, including 86 (53%) women. The median age per country ranged from 3 to 38 years. Cases of S. Chester were more likely to have eaten in a restaurant and visited the coast of Morocco. The results of WGS showed five multilocus sequence types (ST), with 96 of 153 isolates analysed clustering into a tight group that corresponded to a novel ST, ST1954. Of these 96 isolates, 46 (48%) were derived from food or patients returning from Morocco and carried two types of plasmids containing either qnrS1 or qnrB19 genes. This European-wide outbreak associated with travel to Morocco was likely a multi-source outbreak with several food vehicles contaminated by multidrug-resistant S. Chester strains.

Outbreak of Salmonella Enteritidis linked to the consumption of frozen beefburgers received from a food bank and originating from Poland: northern France, December 2014 to April 2015

A prolonged outbreak of Salmonella enterica serotype Enteritidis occurred in northern France between December 2014 and April 2015. Epidemiological investigations following the initial notification on 30 December 2014 of five cases of salmonellosis (two confirmed S. Enteritidis) in young children residing in the Somme department revealed that all cases frequented the same food bank A. Further epidemiological, microbiological and food trace-back investigations indicated frozen beefburgers as the source of the outbreak and the suspected lot originating from Poland was recalled on 22 January 2015. On 2 March 2015 a second notification of S. Enteritidis cases in the Somme reinitiated investigations that confirmed a link with food bank A and with consumption of frozen beefburgers from the same Polish producer. In the face of a possible persistent source of contamination, all frozen beefburgers distributed by food bank A and from the same origin were blocked on 3 March 2015. Microbiological analyses confirmed contamination by S. Enteritidis of frozen beefburgers from a second lot remaining in cases' homes. A second recall was initiated on 6 March 2015 and all frozen beefburgers from the Polish producer remain blocked after analyses identified additional contaminated lots over several months of production.

Community Incidence of Campylobacteriosis and Nontyphoidal Salmonellosis, France, 2008-2013

Community incidence estimates are necessary to assess the burden and impact of infections on health and to set priorities for surveillance, research, prevention, and control strategies. The current study was performed to estimate the community incidence of campylobacteriosis and nontyphoidal salmonellosis in France from the number of laboratory-confirmed cases reported to the national reference center (NRC). The probabilities of a case in the community visiting a doctor, having a stool sample requested, having a positive laboratory test, and having the case reported to the NRC were estimated using data of national surveillance systems, national hospitalization and health insurance databases, and specific surveys informing about these parameters. Credible intervals (CrI) were calculated using Monte Carlo simulation. In addition, we estimated the number of hospitalizations for both infections in France. The annual community incidence rate in France is estimated at 842 cases per 100,000 (90%CrI 525-1690) for campylobacteriosis and 307 cases per 100,000 (90%CrI 173-611) for salmonellosis. The annual number of hospitalizations is estimated at 5182 for campylobacteriosis and 4305 for salmonellosis. The multiplication factors between cases ascertained by the surveillance system and cases in the community were 115 for campylobacteriosis and 20 for salmonellosis. They are consistent with estimates reported in other countries, indicating a high community incidence of campylobacteriosis and salmonellosis in France.