Public health genomics capacity assessment: readiness for large-scale pathogen genomic surveillance in Canada's public health laboratories.

BACKGROUND: Along with rapid diagnostic testing, contact tracing, and public health measures, an effective pandemic response incorporates genomics-based surveillance. Large-scale SARS-CoV-2 genome sequencing is a crucial component of the global response to COVID-19. Characterizing the state of genomics readiness among Canada's public health laboratories was necessary to inform strategic planning and deployment of capacity-building resources in the early stages of the pandemic. METHODS: We used a qualitative study design and focus group discussions, encompassing both technical and leadership perspectives, to perform an in-depth evaluation of the state of pathogen genomics readiness in Canada. RESULTS: We found substantial diversity in the state of readiness for SARS-CoV-2 genomic surveillance across Canada. Despite this variability, we identified common barriers and needs in the areas of specimen access, data flow and sharing, computing infrastructure, and access to highly qualified bioinformatics personnel. CONCLUSIONS: These findings enable the strategic prioritization and deployment of resources to increase Canada's ability to perform effective public health genomic surveillance for COVID-19 and prepare for future emerging infectious diseases. They also provide a unique qualitative research model for use in capacity building.

Determination of Genomic Epidemiology of Historical Clostridium perfringens Outbreaks in New York State by Use of Two Web-Based Platforms: National Center for Biotechnology Information Pathogen Detection and FDA GalaxyTrakr.

Clostridium perfringens is the second leading cause of bacterial foodborne illness in the United States. The Wadsworth Center (WC) at the New York State Department of Health enumerates infectious dose from primary patient and food samples and, until recently, identified C. perfringens to the species level only. We investigated whether whole-genome sequence-based subtyping could benefit epidemiological investigations of this pathogen, as it has with other enteric organisms. We retrospectively sequenced 76 patient and food samples received between May 2010 and February 2020, including 52 samples linked epidemiologically to 13 outbreaks and 24 sporadic samples not linked to other samples. Phylogenetic trees were built using two Web-based platforms: National Centers for Biotechnology Information Pathogen Detection (NCBI-PD) and GalaxyTrakr (a Galaxy instance supported by the GenomeTrakr initiative). For GalaxyTrakr analyses, single nucleotide polymorphism (SNP) matrices and maximum-likelihood (ML) trees were generated using 3 different reference genomes. Across the four separate analyses, phylogenetic clustering was generally concordant with epidemiologically identified outbreaks. SNP diversity among phylogenetically linked samples from an outbreak ranged from 0 to 20 SNPs, excepting one outbreak ranging from 4 to 62 SNPs. Importantly, four of the 13 outbreak isolates harbored one or more samples that were phylogenetic outliers, and for two outbreaks, no samples were closely related. Two specimens were found harboring two distinct genotypes. For samples below CDC enumeration dose threshold, phylogenetic clustering was robust and linked patient and/or food samples. We concluded that WGS phylogenetic clusters (i) are largely concordant with epidemiologically defined outbreaks, irrespective of analysis platform or reference genome we employed; (ii) have limited pairwise SNP diversity, allowing phylogenetic clusters to be distinguished from sporadic cases; and (iii) can aid in epidemiological investigations by identifying outlier and polyclonal samples.

Continual improvement of the pre-analytical process in a public health laboratory with quality indicators-based risk management.

Background Quality indicators (QIs) and risk management are important tools for a quality management system designed to reduce errors in a laboratory. This study aimed to show the effectiveness of QI-based risk management for the continual improvement of pre-analytical processes in the Kayseri Public Health Laboratory (KPHL) which serves family physicians and collects samples from peripheral sampling units. Methods QIs of pre-analytical process were used for risk assessment with the failure modes and effects analysis (FMEA) method. Percentages and risk priority numbers (RPNs) of QIs were quantified. QI percentages were compared to the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) performance specifications and RPNs were compared to risk level scale, and corrective actions planned if needed. The effectiveness of risk treatment actions was re-evaluated with the new percentages and with RPNs of predefined QIs. Results RPNs related to four QIs required corrective action according to the risk evaluation scale. After risk treatment, the continual improvement was achieved for performance and risk level of "transcription errors", for risk levels of "misidentified samples" and "not properly stored samples" and for the performance of "hemolyzed samples". "Not properly stored samples" had the highest risk score because of sample storage and centrifugation problems of peripheral sampling units which are not under the responsibility of the KPHL. Conclusions Public health laboratories may have different risk priorities for pre-analytical process. Risk management based on predefined QIs can decrease the risk levels and increase QI performance as evidence-based examples for continual improvement of the pre-analytical process.

Capacity assessment of the health laboratory system in two resource-limited provinces in China.

BACKGROUND: Strong laboratory capacity is essential for detecting and responding to emerging and re-emerging global health threats. We conducted a quantitative laboratory assessment during 2014-2015 in two resource-limited provinces in southern China, Guangxi and Guizhou in order to guide strategies for strengthening core capacities as required by the International Health Regulations (IHR 2005). METHODS: We selected 28 public health and clinical laboratories from the provincial, prefecture and county levels through a quasi-random sampling approach. The 11-module World Health Organization (WHO) laboratory assessment tool was adapted to the local context in China. At each laboratory, modules were scored 0-100% through a combination of paper surveys, in-person interviews, and visual inspections. We defined module scores as strong (> = 85%), good (70-84%), weak (50-69%), and very weak (< 50%). We estimated overall capacity and compared module scores across the provincial, prefecture, and county levels. RESULTS: Overall, laboratories in both provinces received strong or good scores for 10 of the 11 modules. These findings were primarily driven by strong and good scores from the two provincial level laboratories; prefecture and county laboratories were strong or good for only 8 and 6 modules, respectively. County laboratories received weak scores in 4 modules. The module, 'Public Health Functions' (e.g., surveillance and reporting practices) lagged far behind all other modules (mean score = 46%) across all three administrative levels. Findings across the two provinces were similar. CONCLUSIONS: Laboratories in Guangxi and Guizhou are generally performing well in laboratory capacity as required by IHR. However, we recommend targeted interventions particularly for county-level laboratories, where we identified a number of gaps. Given the importance of surveillance and reporting, addressing gaps in public health functions is likely to have the greatest positive impact for IHR requirements. The quantitative WHO laboratory assessment tool was useful in identifying both comparative strengths and weaknesses. However, prior to future assessments, the tool may need to be aligned with the new WHO IHR monitoring and evaluation framework.

[Situation of public laboratories manufacturing antivenoms in Latin AmericaA situação dos laboratórios públicos produtores de soros antivenenos na América Latina]. / Situación de los laboratorios públicos productores de antivenenos en América Latina.

The situation of public laboratories manufacturing antivenoms in Latin America was analyzed, based on the results of a workshop coordinated by the Pan American Foot-and-Mouth Disease Center (PANAFTOSA) of the Pan American Health Organization (PAHO). Nine countries in the region have 12 public laboratories that produce and distribute antivenoms for use against different venomous animals. The situation of each laboratory was discussed, and an analysis was conducted of the current scenario, which is characterized by increasing regulatory requirements that vary in terms of infrastructure and production capacity. The authors identified a need to organize regional cooperation processes to improve the availability of antivenoms, including: research and development projects to improve processes and technologies; studies of the capacity of antivenoms to neutralize different poisons; and technical training programs for professionals and technical personnel. In the current context, in which the World Health Organization has prepared a global strategy for the prevention and control of snakebite envenoming, PANAFTOSA has taken on coordination of this initiative in the Americas. Improving the availability of antivenoms is the priority. As a result of the workshop, the RELAPA network was created, bringing together public laboratories that manufacture antivenoms in Latin America, in order to strengthen these laboratories and increase the availability of, and access to effective and safe antivenoms throughout Latin America.

A situação dos laboratórios públicos produtores de soros antivenenos na América Latina foi analisada com base nas conclusões de um seminário coordenado pelo Centro Pan-Americano de Febre Aftosa (PANAFTOSA) da Organização Pan-Americana da Saúde (OPAS). Em nove países da Região, encontram-se 12 laboratórios públicos que produzem e distribuem soros contra venenos de diferentes animais peçonhentos. Examinou-se a situação de cada laboratório, analisou-se o panorama atual marcado por crescentes demandas de regulação e pela heterogeneidade da infraestrutura e capacidade produtiva dos laboratórios e destacou-se a necessidade de um esforço concertado de cooperação regional com vistas a aumentar a disponibilidade de soros antivenenos, englobando projetos de pesquisa e desenvolvimento para o avanço dos processos e tecnologias, estudos do perfil da capacidade de neutralização dos soros contra diversos venenos e programas de capacitação técnica de profissionais e pessoal técnico. No contexto atual, em que uma estratégia mundial de prevenção e controle de acidentes ofídicos foi elaborada pela Organização Mundial da Saúde e que a coordenação das ações relacionadas na Região das Américas foi assumida pelo PANAFTOSA, melhorar a disponibilidade de soros antivenenos é prioridade. Como resultado deste seminário, a Rede de Laboratórios Públicos Produtores de Soros Antivenenos da América Latina (RELAPA) foi formada com o objetivo de fortalecer os laboratórios e aumentar a disponibilidade e a acessibilidade de soros antivenenos eficazes e seguros em toda América Latina.

Bioinformatic Analyses of Whole-Genome Sequence Data in a Public Health Laboratory.

The ability to generate high-quality sequence data in a public health laboratory enables the identification of pathogenic strains, the determination of relatedness among outbreak strains, and the analysis of genetic information regarding virulence and antimicrobial-resistance genes. However, the analysis of whole-genome sequence data depends on bioinformatic analysis tools and processes. Many public health laboratories do not have the bioinformatic capabilities to analyze the data generated from sequencing and therefore are unable to take full advantage of the power of whole-genome sequencing. The goal of this perspective is to provide a guide for laboratories to understand the bioinformatic analyses that are needed to interpret whole-genome sequence data and how these in silico analyses can be implemented in a public health laboratory setting easily, affordably, and, in some cases, without the need for intensive computing resources and infrastructure.

Rapid whole-genome sequencing for surveillance of Salmonella enterica serovar enteritidis.

For Salmonella enterica serovar Enteritidis, 85% of isolates can be classified into 5 pulsed-field gel electrophoresis (PFGE) types. However, PFGE has limited discriminatory power for outbreak detection. Although whole-genome sequencing has been found to improve discrimination of outbreak clusters, whether this procedure can be used in real-time in a public health laboratory is not known. Therefore, we conducted a retrospective and prospective analysis. The retrospective study investigated isolates from 1 confirmed outbreak. Additional cases could be attributed to the outbreak strain on the basis of whole-genome data. The prospective study included 58 isolates obtained in 2012, including isolates from 1 epidemiologically defined outbreak. Whole-genome sequencing identified additional isolates that could be attributed to the outbreak, but which differed from the outbreak-associated PFGE type. Additional putative outbreak clusters were detected in the retrospective and prospective analyses. This study demonstrates the practicality of implementing this approach for outbreak surveillance in a state public health laboratory.

Salmonella Grumpensis Causing Diarrhea in Children - Shanghai Municipality, China, 2023.

What is already known about this topic?: Foodborne diseases are a growing public health concern with a notable disease burden in China. What is added by this report?: Two children with diarrhea visited a healthcare facility within 24 hours on August 1 and 2, 2023. Salmonella Grumpensis was detected in their stool samples by the public health laboratory. Whole genome sequencing (WGS) analysis revealed characteristics typical of outbreak strains. Although the origin of the outbreak was unknown, the possibility of a hidden shared infection was deemed feasible. What are the implications for public health practice?: It underscores the importance of thorough genomic surveillance to promptly detect emerging pathogens. Public health laboratories play a crucial role by utilizing advanced genomic technologies for accurate pathogen identification and timely warning systems.

Providing specimen transport through an online marketplace in the Northern region of Ghana.

Background: Integrated diagnostic networks, which are themselves dependent on robust specimen transport solutions, are fundamental to effective healthcare systems. Objective: This study aimed to pilot an online marketplace for the transport of specimens throughout a laboratory network in Ghana. Methods: Independent drivers were matched with health facilities that required specimen transport using a suite of mobile applications and web portals developed for this study. This marketplace was piloted with seven drivers, two laboratories, and five health facilities in Ghana's Northern region from March 2019 to October 2019. Results: During the pilot, 182 deliveries were completed for 691 patients, including 4118 laboratory tests for antenatal care, disease surveillance, and clinical testing. Testing included 34 tests for communicable and non-communicable diseases. All but two specimens (laboratory cancellations) were successfully delivered and tested. The median time from request to encrypted emailing of results was 19.7 h, while that for a drop-off request was 0.9 h. In the midwife registry, the median time from patient visit to result recording was 1 day, compared to 4 days in the same months in 2018, and the number of mothers without documented testing decreased from 41 to 3. Similarly, the proportion of tuberculosis specimen deliveries from Buipe Polyclinic to Tamale Zonal Laboratory taking over 1 day fell from 62% at baseline to 3% during the pilot. Conclusion: An online marketplace successfully orchestrated the delivery of laboratory specimens under a variety of clinical circumstances, reducing overall turn-around time without diminution of the overall specimen delivery process. What this study adds: This study established the efficacy of an online marketplace to orchestrate timely and high-quality delivery of specimens within a laboratory network.

Has Data Quality of an Antimicrobial Resistance Surveillance System in a Province of Nepal Improved between 2019 and 2022?

An operational research study was conducted in 2019 to assess the quality of data submitted by antimicrobial resistance (AMR) surveillance sites in the Bagmati Province of Nepal to the National Public Health Laboratory for Global Antimicrobial Resistance and Use Surveillance System (GLASS). Measures were implemented to enhance the quality of AMR surveillance by strengthening capacity, improving infrastructure, implementing data sharing guidelines, and supervision. The current study examined reports submitted by surveillance sites in the same province in 2022 to assess whether the data quality had improved since 2019. The availability of infrastructure at the sites was assessed. Of the nine surveillance sites in the province, seven submitted reports in 2022 versus five in 2019. Completeness in reporting improved significantly from 19% in 2019 to 100% in 2022 (p < 0.001). Timely reports were received from two sites in 2019 and only one site in 2022. Specimen-pathogen consistency in accordance with the GLASS guidelines for urine, feces, and genital swab specimens improved, with ≥90% consistency at all sites. Overall, the pathogen-antibacterial consistency improved significantly for each GLASS priority pathogen. The study highlights the importance of dedicated infrastructure and institutional arrangements for AMR surveillance. Similar assessments covering all provinces of the country can provide a more complete country-wide picture.

Postmortem genetic testing in sudden unexplained death: A public health laboratory experience.

Sudden unexplained death in the young poses a diagnostically challenging situation for practicing autopsy pathologists, especially in the absence of anatomic and toxicological findings. Postmortem genetic testing may identify pathogenic variants in the deceased of such cases, including those associated with arrhythmogenic channelopathies and cardiomyopathies. The Wisconsin State Laboratory of Hygiene (WSLH) is a state-run public health laboratory which performs postmortem genetic testing at no cost to Wisconsin medical examiners and coroners. The current study examines sequencing data from 18 deceased patients (ages 2 months to 49 years, 5 females) submitted to WSLH, from 2016 to 2021. Panel-based analysis was performed on 10 cases, and whole exome sequencing was performed on the most recent 8 cases. Genetic variants were identified in 14 of 18 decedents (77.8%), including 7 with pathogenic or likely pathogenic variants (38.9%). Whole exome sequencing was more likely to yield a positive result, more variants per decedent, and a larger number of variants of uncertain significance. While panel-based testing may offer definitive pathogenic variants in some cases, less frequent variants may be excluded. Whole exome testing may identify rare variants missed by panels, but increased yield of variants of uncertain significance may be difficult to interpret. Postmortem genetic testing in young decedents of sudden unexplained death can provide invaluable information to autopsy pathologists to establish accurate cause and manner of death and to decedent's relatives to allow appropriate management. A public health laboratory model may be a financially advisable alternative to commercial laboratories for medical examiner's/coroner's offices.

Surveillance and laboratory collaboration in response to an outbreak of Vibrio parahaemolyticus, Plesiomonas shigelloides, and Aeromonas hydrophila in Sekondi-Takoradi, Ghana: a case series.

BACKGROUND: The detection of epidemic-prone pathogens is important in strengthening global health security. Effective public health laboratories are critical for reliable, accurate, and timely testing results in outbreak situations. Ghana received funding as one of the high-risk non-Ebola affected countries to build and strengthen public health infrastructure to meet International Health Regulation core capacities. A key objective was to build laboratory capacities to detect epidemic-prone diseases. CASE PRESENTATION: In June 2018, a local hospital received eight patients who presented with acute diarrhea. A sample referral system for Ghana has not been established, but the Sekondi Zonal Public Health Laboratory staff and mentors collaborated with Disease Surveillance Officers (DSOs) to collect, package, and transport stool specimens from the outbreak hospital to the Public Health Laboratory for laboratory testing. The patients included seven females and one male, of Fante ethnicity from the Fijai township of Sekondi-Takoradi Municipality. The median age of the patients was 20 years (interquartile range: 20-29 years). Vibrio parahaemolyticus was identified within 48 hours from four patients, Plesiomonas shigelloides from one patient, and Aeromonas hydrophila from another patient. There was no bacteria growth from the samples from the two other patients. All patients were successfully treated and discharged. CONCLUSION: This is the first time these isolates have been identified at the Sekondi Zonal Public Health Laboratory, demonstrating how rapid response, specimen transportation, laboratory resourcing, and public health coordination are important in building capacity towards achieving health security. This capacity building was part of the United States Centers for Disease Control and Prevention engagement of international and local partners to support public health laboratories with supplies, diagnostic equipment, reagents, and logistics.

Lessons learned for public health workforce development: An evaluation of the centers for disease control and prevention's laboratory leadership service fellowship.

The Centers for Disease Control and Prevention launched the Laboratory Leadership Service (LLS) Fellowship Program in July 2015 to develop public health laboratory (PHL) leaders who will improve PHL quality and safety. This article describes a retrospective, summative evaluation to determine the extent to which LLS has met its short-term goals for PHL workforce development. The evaluation relied on existing data from routine LLS data collection and reporting, supplemented with a new alumni survey. The purpose of the design was threefold: 1) to reduce data collection burden on program staff and participants, 2) to assess the value and limits of routine fellowship data for comprehensive public health workforce development program evaluation, and 3) to identify ways to improve LLS's routine data collections for program evaluation. We used descriptive statistics, qualitative analysis, and participatory methods (i.e., a data party) to analyze and interpret data. Results show LLS short-term outcome achievement and highlight opportunities for program improvement, particularly related to the design of certain training requirements and for future evaluations. Overall, the evaluation contributes to lessons learned for PHL workforce development efforts, including how routine data collections can contribute to comprehensive public health workforce development evaluations.

Common bacteria in sputum or gastric lavage of patients presenting with signs and symptoms of lower respiratory tract infections.

INTRODUCTION: lower respiratory tract infections (LRTIs) are infections involving the trachea, primary bronchi and lungs. People with LRTIs typically experience coughs as the primary symptoms; however, shortness of breath, weakness, fever and fatigue may be coupled with the cough. It is common among the aged, children under five and the immune-suppressed. Persons with symptoms suggestive of pulmonary tuberculosis (TB) may have tuberculosis, other respiratory tract infection or co-infection of tuberculosis and other respiratory pathogens. This study aimed to identify the presence of pathogens in sputum of suspected tuberculosis cases and their antimicrobial resistance patterns. METHODS: this was a retrospective study conducted from September 2018 to November 2019 at Tamale Public Health Laboratory. Sputum or gastric lavage samples were collected from persons with suspected clinical presentations of TB and/or LRTI. These samples were cultured using standard microbiological protocols and antimicrobial susceptibility test performed on the positive cultures by Kirby-Bauer disc diffusion method. Molecular identification of M. tuberculosis was performed on all the suspected TB cases using GeneXpert mycobacterium tuberculosis/rifampin (MTB/RIF) assay. RESULTS: during the study period, there were 264 cases of which 49.2% were males and 50.8% were females. Positive cases for culture were 47.3%. Out of the 264 cases, 186 (70.5%) were suspected TB with 51.6% being positive for culture, 6.5% positive for M. tuberculosis (GeneXpert confirmed) and 3.8% co-infection of TB with other bacteria pathogens. Klebsiella spp. (35/125; 28%) and Pseudomonas spp. (19/125; 15.2%) were the most predominant pathogens isolated. There was no significant difference in detection of bacteria in males and females (p=0.89), however individuals with suspected TB were significantly infected with other bacterial species than the unsuspected individuals (p=0.03). Almost all the isolates showed high susceptibility towards carbapenem (meropenem) and high resistance towards the third generation cephalosporins (cefotaxime and ceftriaxone). CONCLUSION: this study highlights the need to test individuals with classical symptoms of LRTIs for other bacterial infections other than TB only. Sputum culture is recommended for all suspected tuberculosis cases to provide accurate laboratory diagnosis to LRTIs and mitigate unnecessary use of antimicrobials.

Quality management system implementation in human and animal laboratories.

BACKGROUND: The ability to rapidly detect emerging and re-emerging threats relies on a strong network of laboratories providing high quality testing services. Improving laboratory quality systems to ensure that these laboratories effectively play their critical role using a tailored stepwise approach can assist them to comply with the World Health Organization's (WHO) International Health Regulations (IHRs) and the World Organization for Animal Health's (OIE) guidelines. METHODS: Fifteen (15) laboratories in Armenia's human and veterinary laboratory networks were enrolled into a quality management system strengthening programme from 2017 to 2020. Training was provided for key staff, resulting in an implementation plan developed to address gaps. Routine mentorship visits were conducted. Audits were undertaken at baseline and post-implementation using standardised checklists to assess laboratory improvements. RESULTS: Baseline audit general indicator scores ranged from 21% to 46% for human laboratories and 37% to 60% for the veterinary laboratories. Following implementation scores improved ranging from 7 to 39% for human laboratories and 12% to 19% for veterinary laboratories. CONCLUSION: In general, there has been improvement for both human and veterinary laboratories in the areas of QMS implementation, particularly in organizational structure, human resources, equipment management, supply chain and data management. Central facilities developed systems that are ready for international accreditation. This One Health strengthening project ensured simultaneous strengthening of both human and veterinary laboratories which is not a common approach.

Laboratory response checklist for infectious disease outbreaks-preparedness and response considerations for emerging threats.

The purpose of the Laboratory Response Checklist for Infectious Disease Outbreaks (the Checklist) is to provide public health laboratories and laboratory networks operating at multiple jurisdictional levels with a useful, adaptable tool to help rapidly identify important outbreak response considerations, particularly when investigating a previously unknown infectious disease threat. The Checklist was developed by the National Microbiology Laboratory of Canada in collaboration with provincial/territorial, national and international laboratory experts, including the Canadian Public Health Laboratory Network, and the Global Health Security Action Group Laboratory Network. While the Checklist was initially designed to reflect lessons learned through National Microbiology Laboratory participation in extended national and international outbreak responses (e.g. Zika virus epidemic [2015-2016], Ebola virus epidemic, West Africa [2014-2016]), the importance of optimizing laboratory response coordination has only been underscored by the ongoing challenges presented by the coronavirus disease 2019 (COVID-19) pandemic response requirements. The Checklist identifies five highly interdependent laboratory response themes, each of which encompasses multiple considerations that may be critical to a coordinated, strategic outbreak response. As such, the comprehensive review of Checklist considerations by responding laboratory organizations may provide a valuable opportunity to quickly detect key response considerations and interdependencies, and mitigate risks with the potential to impact public health action.

Strengthening laboratory capacity for detection of respiratory viral pathogens through the Global Health Security Agenda (GHSA) framework.

BACKGROUND: Endemic and emerging respiratory viruses are a threat to public health, and a robust public health laboratory system is essential to ensure global health security. OBJECTIVE: This program sought to expand molecular laboratory testing capacity to detect a broad range of respiratory pathogens in clinical respiratory specimens collected during disease surveillance and outbreak investigations. METHODS: As a part of the Global Health Security Agenda (GHSA), the United States Centers for Disease Control and Prevention utilised the equipment and training infrastructure already in place at the World Health Organization National Influenza Centers to expand testing capacity for respiratory viruses in laboratories in GHSA partner countries. This was done through the provision of quality assured reagents, including multiplex platforms and technical guidance for laboratory staff, as well as the assessment of laboratory testing accuracy. CONCLUSION: Early findings illustrated that GHSA laboratories have been able to expand testing capacity using specimens from routine surveillance, as well as from outbreak situations.

Whole Genome Sequencing Based Surveillance of L. monocytogenes for Early Detection and Investigations of Listeriosis Outbreaks.

In Austria, all laboratories are legally obligated to forward human and food/environmental L. monocytogenes isolates to the National Reference Laboratory/Center (NRL) for Listeria. Two invasive human isolates of L. monocytogenes serotype 1/2a of the same pulsed-field gel electrophoresis (PFGE) pattern, previously unknown in Austria, were cultured for the first time in January 2016. Five further human isolates, obtained from patients with invasive listeriosis between April 2016 and September 2017, showed this PFGE pattern. In Austria the NRL started to use whole-genome sequencing (WGS) based typing in 2016, using a core genome MLST (cgMLST) scheme developed by Ruppitsch et al. 2015, which contains 1701 target genes. Sequence data are submitted to a publicly available nomenclature server (Ridom GmbH, Münster, Germany) for allocation of the core genome complex type (CT). The seven invasive human isolates differed from each other with zero to two alleles and were allocated to CT1234 (declared as outbreak strain). Among the Austrian strain collection of about 6,000 cgMLST-characterized non-human isolates (i.e., food/environmental isolates) 90 isolates shared CT1234. Out of these, 83 isolates were traced back to one meat processing-company. They differed from the outbreak strain by up to seven alleles; one isolate originated from the company's industrial slicer. The remaining seven CT1234-isolates were obtained from food products of four other companies (five fish-products, one ready-to-eat dumpling and one deer-meat) and differed from the outbreak strain by six to eleven alleles. The outbreak described shows the considerable potential of WGS to identify the source of a listeriosis outbreak. Compared to PFGE analysis, WGS-based typing has higher discriminatory power, yields better data accuracy, and allows higher laboratory through-put at lower cost. Utilization of WGS-based typing results of human and food/ environmental L. monocytogenes isolates by appropriate public health analysts and epidemiologists is indispensable to support a successful outbreak investigation.

One health approach in Nepal: Scope, opportunities and challenges.

One Health (OH) is a collaborative effort to attain optimal health for people, animals and the environment. The concept of OH is still in its infancy in Nepal but is increasingly growing. The Government of Nepal (GoN) has taken some initiatives to tackle burgeoning problems such as antimicrobial resistance, highly pathogenic avian influenza and rabies using OH approach but there are several challenges at the level of implementation. Few non-governmental organizations support GoN to promote an OH approach. The major bottlenecks in implementing OH in Nepal include poor organizational structure to support OH, absence of a legal framework to implement OH, poor coordination among different governmental agencies, insufficient technical expertise, poor data sharing mechanism across sectors, limited budget and poor understanding at political level. We encourage GoN to address these gaps and prioritize the health problems where OH approach would give the best outcome. Institutional and legal frameworks need to be created to effectively implement an OH approach in Nepal. Increasing awareness among policy makers including political leadership and increasing regular government budget for OH activities would be helpful to promote OH in Nepal.

An overview of the National Microbiology Laboratory emergency management program.

The National Microbiology Laboratory (NML) emergency management program was developed after the 2003 Severe Acute Respiratory Syndrome (SARS) outbreak to provide a framework for the responses to public health events. The program comprises three components (Site response, Continuity and Site support) that have adopted the Incident Command System (ICS) as their management structure and follows the four phases of emergency management. All program components have extensive competency-based training for staff and exercise plans. The emergency management program ensures quality and continuous improvement through its certification in International Organization for Standardization (ISO) 9001 and structured review processes. This means that the Operations Centre can be activated and working at optimum capacity with highly trained and experienced staff within an hour of receiving notice to begin a response. The NML can also send mobile laboratories to aid Canadian or international efforts to address outbreaks or bioterrorism events.