The onset of the COVID-19 pandemic triggered a rapid scale-up in the use of genomic surveillance as a pandemic preparedness and response tool. As a result, the number of countries with in-country SARS-CoV-2 genomic sequencing capability increased by 40% from February 2021 to July 2022. The Global Genomic Surveillance Strategy for Pathogens with Pandemic and Epidemic Potential 2022-2032 was launched by the World Health Organization (WHO) in March 2022 to bring greater coherence to ongoing work to strengthen genomic surveillance. This paper describes how WHO\'s tailored regional approaches contribute to expanding and further institutionalizing the use of genomic surveillance to guide pandemic preparedness and response measures as part of a harmonized global undertaking. Challenges to achieving this vision include difficulties obtaining sequencing equipment and supplies, shortages of skilled staff, and obstacles to maximizing the utility of genomic data to inform risk assessment and public health action. WHO is helping to overcome these challenges in collaboration with partners. Through its global headquarters, six regional offices, and 153 country offices, WHO is providing support for country-driven efforts to strengthen genomic surveillance in its 194 Member States, with activities reflecting regional specificities. WHO\'s regional offices serve as platforms for those countries in their respective regions to share resources and knowledge, engage stakeholders in ways that reflect national and regional priorities, and develop regionally aligned approaches to implementing and sustaining genomic surveillance within public health systems.

UNASSIGNED: Since 2007, national public health laboratories in the WHO Eastern Mediterranean Region (EMR) have participated in a regional external quality assessment scheme in bacteriology to improve testing proficiency.
UNASSIGNED: To assess laboratory performance in bacteriology in the EMR between 2011 and 2019 using the regional external quality assessment scheme.
UNASSIGNED: We analysed the accuracy of participant-reported data in bacterial identification, Gram stain microscopy, and antimicrobial susceptibility testing. For each category, we assessed the performance over time, the performance on multiple organisms, and whether a laboratory repeatedly failed to attain satisfactory results.
UNASSIGNED: Between 2011 and 2019, 70% of laboratories achieved satisfactory performance for bacterial identification and antimicrobial susceptibility testing, and 85% performed satisfactory Gram stain microscopy. Testing did not improve on multiple organisms and results were consistently low for some pathogens and test categories. Twenty-nine percent of laboratories underperformed throughout the study period.
UNASSIGNED: The unchanged performance over time and underperformance of laboratories highlight the need for improvements in the regional external quality assessment scheme. Participating laboratories and WHO need to work more actively to strengthen the problem areas.
التقييم الخارجي لجودة أداء المختبرات المتخصصة في علم الجراثيم في إقليم شرق المتوسط، 2011–2019.
همايون أصغر، كارين نهابتيان، أماني غنيم، فرانك كونينجز، أمينة الجرداني.
UNASSIGNED: منذ عام 2007 ، شاركت مختبرات الصحة العامة الوطنية في إقليم شرق المتوسط في مخطط إقليمي للتقييم الخارجي للجودة في علم الجراثيم لتحسين كفاءة الاختبارات.
UNASSIGNED: هدفت هذه الدراسة الى تقييم أداء المختبرات في مجال علم الجراثيم في إقليم شرق المتوسط بين عامَي 2011 و 2019 ، باستخدام النظام الإقليمي للتقييم الخارجي للجودة.
UNASSIGNED: حللنا دقة البيانات التي أبلغ بها المشاركون فيما يخص تحديد الجراثيم، والفحص المجهري لصبغة جرام، واختبار الحساسية لمضادات الميكروبات. وبالنسبة إلى كل فئة، قيمنا الأداء مع مرور الزمن، والأداء على كائنات حية متعددة، وما إذا كان المختبر قد فشل مرارًا في تحقيق نتائج مُرضية.
UNASSIGNED: بين عامَي 2011 و 2019 ، حقق 70 ٪ من المختبرات أداءً مُرضيًا في التعرف على الجراثيم وتحديدها واختبار الحساسية لمضادات الميكروبات، ونفذ 85 ٪ منها الفحصَ المجهري لصبغة جرام تنفيذًا مُرضيًا. ولم يتحسن مستوى الاختبار على كائنات حية متعددة، وكانت النتائج منخفضة باستمرار فيما يخص بعض مسببات الأمراض وفئات الاختبارات. وكان أداء 29 ٪ من المختبرات دون المستوى خلال فترة الدراسة.
UNASSIGNED: إن عدم تغيُُّّر الأداء بمرور الوقت والأداء القاصر للمختبرات يبرزان الحاجة إلى إدخال تحسينات على الخطة الإقليمية للتقييم الخارجي للجودة. لذا، يتعيََّّن على المختبرات المشارِكة و المختبرات المشاركة ومنظمة الصحة العالمية بحاجة إلى العمل بشكل أكثر نشاطا لتقوية مناطق المشاكل.
Évaluation externe de la qualité des performances des laboratoires en bactériologie dans la Région de la Méditerranée orientale, 2011-2019.
UNASSIGNED: Depuis 2007, les laboratoires de santé publique nationaux de la Région OMS de la Méditerranée orientale ont participé à un système régional d\'évaluation externe de la qualité en bactériologie afin d\'améliorer la bonne exécution des analyses.
UNASSIGNED: Évaluer les performances des laboratoires en bactériologie dans la Région de la Méditerranée orientale entre 2011 et 2019 à l\'aide du système régional d\'évaluation externe de la qualité.
UNASSIGNED: Nous avons analysé l\'exactitude des données communiquées par les participants concernant l\'identification bactérienne, la microscopie après coloration de Gram et les tests de sensibilité aux antimicrobiens. Pour chaque catégorie, nous avons évalué la performance au fil du temps, la performance sur plusieurs micro-organismes et avons vérifié si un laboratoire n\'a pas obtenu des résultats satisfaisants à plusieurs reprises.
UNASSIGNED: Entre 2011 et 2019, 70 % des laboratoires ont obtenu des résultats satisfaisants pour l\'identification bactérienne et les tests de sensibilité aux antimicrobiens, et 85 % ont effectué une microscopie après coloration de Gram satisfaisante. Les tests ne se sont pas améliorés sur plusieurs micro-organismes et les résultats étaient systématiquement faibles pour certains agents pathogènes et certaines catégories de tests. Vingt-neuf pour cent des laboratoires ont eu des résultats insuffisants tout au long de la période d\'étude.
UNASSIGNED: Les performances inchangées au cours du temps et les résultats insuffisants des laboratoires soulignent la nécessité d\'améliorer le système régional d\'évaluation externe de la qualité. Les laboratoires participants et l\'OMS doivent collaborer plus activement pour renforcer les domaines qui posent problème.

In early 2020, COVID-19 exposed differences in public health laboratory systems\' testing abilities. Focusing on Germany, the USA and the UK between 1900 and 2020, this article argues that studying the distinct evolution of laboratory infrastructures is critical to understanding the history of infection control and the limits of template-based reforms in global health. While each analysed laboratory infrastructure was shaped by a unique national context, neoliberal visions of lean public services and declining resources led to significant reform pressure from the 1970s. The US Center of Disease Control\'s model of epidemic intelligence provided an attractive template to integrate resources and focus planning on preparedness scenarios. It also helped justify cuts to local laboratory infrastructures. Effects were uneven: in the USA and the UK, improved integration failed to compensate for local laboratory cuts and loss of autonomy. By contrast, Germany\'s subsidiary principle allowed for limited federal integration while leaving local services mostly intact.

During the COVID-19 pandemic, state newborn screening programs faced challenges to ensure this essential public health program continued to function at a high level. In December 2020, the EveryLife Foundation for Rare Diseases held a workshop to discuss these common challenges and solutions. Newborn screening officials described challenges including short staffing across the entire program, collection and transport of specimens, interrupted follow-up activities, and pilot study recruitment. To address these challenges, state programs implemented a wide variety of solutions to maintain the high standards of newborn screening. To address staffing issues, newborn screening programs, public health laboratories, and hospitals all cross-trained personnel, worked to manage staff stress, and established essential functions. Other solutions included working with courier companies to ensure the timely pick-up of specimen, creating educational materials for hospital staff, and the creation of hybrid recruitment models for pilot studies. Implementing the lessons discussed throughout this paper can help to prepare for the next public health emergencies to ensure that a program that interacts with millions of families every year and saves the lives of thousands of children every year is minimally impacted.

Public health laboratories (PHLs) continue to face internal and external challenges to their abilities to provide successful, timely responses to public health crises and emerging threats. These laboratories are mandated to maintain the health of their communities by identifying, diagnosing, and warning constituents of potential and real health emergencies. Due to the changing characteristics of public health threats and their cross-jurisdictional nature, laboratories are facing increased pressure to ensure that they respond in a consistent and coordinated manner. Here, the Association of Public Health Laboratories (APHL) Emerging Leader Program Cohort 11 members have compiled stories from subject matter experts (SMEs) at PHLs with direct involvement in crises to determine the characteristics of a successful response. Experts examined a diverse selection of emerging threats from across PHLs, including infectious diseases, opioids, natural disasters, and government shutdowns. While no public health crisis will be identical to another, overarching themes were consistent across subjects. Experiences from SMEs that could improve future responses to emerging threats are highlighted.

BACKGROUND: Proper detection of disease-causing organisms is very critical in controlling the course of outbreaks and avoiding large-scale epidemics. Nonetheless, availability of resources to address these gaps have been difficult due to limited funding. This report sought to highlight the importance of in-country partners and non-governmental organizations in improving detection of microbiological organisms in Ghanaian Public Health Laboratories (PHLs).
UNASSIGNED: This study was conducted between June, 2018 to August, 2019. U. S CDC engaged the Centre for Health Systems Strengthening (CfHSS) through the Association of Public Health Laboratories to design and implement strategies for strengthening three PHLs in Ghana. An assessment of the three PHLs was done using the WHO/CDS/CSR/ISR/2001.2 assessment tool. Based on findings from the assessments, partner organizations (CfHSS/APHL/CDC) serviced and procured microbiological equipment, laboratory reagents and logistics. CfHSS provided in-house mentoring and consultants to assist with capacity building in detection of epidemic-prone infectious pathogens by performing microbiological cultures and antimicrobial susceptibility tests.
RESULTS: A total of 3902 samples were tested: blood (1107), urine (1742), stool (249) and cerebrospinal fluid (CSF) (804). All-inclusive, 593 pathogenic bacteria were isolated from blood cultures (70; 11.8%); urine cultures (356; 60%); stool cultures (19; 3.2%) and from CSF samples (148; 25%). The most predominant pathogens isolated from blood, urine and stool were Staphylococcus aureus (22/70; 31%), Escherichia coli (153/356; 43%) and Vibrio parahaemolyticus (5/19; 26.3%), respectively. In CSF samples, Streptococcus pneumoniae was the most frequent pathogen detected (80/148; 54.1%). New bacterial species such as Pastuerella pneumotropica, Klebsiella oxytoca, Vibrio parahaemolyticus, and Halfnia alvei were also identified with the aid of Analytical Profile Index (API) kits that were introduced as part of this implementation. Streptococcus pneumoniae and Neisseria meningitidis detections in CSF were highest during the hot dry season. Antimicrobial susceptibility test revealed high rate of S. aureus, K. pneumoniae and E. coli resistance to gentamicin (35-55%). In urine, E. coli was highly resistant to ciprofloxacin (39.2%) and ampicillin (34%).
CONCLUSIONS: Detection of epidemic-prone pathogens can be greatly improved if laboratory capacity is strengthened. In-country partner organizations are encouraged to support this move to ensure accurate diagnosis of diseases and correct antimicrobial testing.

Next-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories. However, costs of operation and the need for specialized staff remain major hurdles for laboratories with limited resources for implementing these technologies. This project aimed to assess the feasibility of using Oxford Nanopore MinION whole-genome sequencing data of Mycobacterium tuberculosis isolates for species identification, in silico spoligotyping, detection of mutations associated with antimicrobial resistance (AMR) to accurately predict drug susceptibility profiles, and phylogenetic analysis to detect transmission between cases. The results were compared prospectively in real time to those obtained with our current clinically validated Illumina MiSeq sequencing assay for M. tuberculosis and phenotypic drug susceptibility testing results when available. Our assessment of 431 sequenced samples over a 32-week period demonstrates that, when using the proper quality controls and thresholds, the MinION can achieve levels of genotyping analysis and phenotypic resistance predictions comparable to those of the Illumina MiSeq at a very competitive cost per sample. Our results indicate that nanopore sequencing can be a suitable alternative to, or complement, currently used sequencing platforms in a clinical setting and has the potential to be widely adopted in public health laboratories in the near future.

OBJECTIVE: This study aimed at identifying the needs for the health workforce in 16 public health laboratories in the Serbian capital by assessing the workforce stock, workload activities, activity standards, and workload pressure.
METHODS: A review of laboratory records and regulations, interviews with key respondents, and observing work processes provided data for the World Health Organization method for determining staffing needs based on workload indicators (Workload Indicators of Staffing Need, WISN).
RESULTS: A total of 99 laboratory workers spend almost 70% of their available working time in undertaking core activities. Core activities per sample can take from 0.25 to 180 min. Laboratory workers are under moderate or high workload pressure (the WISN ratio from 0.86 to 0.50). The WISN difference indicates a shortage of 22.22% of laboratory analysts and 20.63% of laboratory technicians. To balance the staffing to workload, these laboratories need an additional 8 FTE analysts and 13 FTE technicians. They could also consider selectively reducing workload pressure by automating some of the additional activities while maintaining the competence of laboratory workers and opportunities for professional development.
CONCLUSIONS: Staffing policy should account for work processes, activity standards, and workload pressure to determine necessary staffing to meet the need for laboratory services in the local context.

The 2014 Ebola outbreak revealed biosafety vulnerabilities across the United States. We distributed $24.1 million to health departments to support public health laboratories (PHLs) and sentinel clinical laboratory partners to improve biosafety practices. We used 9 indicators to evaluate PHLs and associated clinical laboratories from March 2015 through April 2018 using descriptive statistics. On average, over 6 reporting periods, 59 awardee PHLs and 4,040 clinical laboratories responded. By April 2018, 92% (57 of 62) of PHLs had conducted at least 1 risk assessment for work with Ebola and another highly infectious disease. The number of PHLs having a policy for risk assessments increased from 32 of 61 (52%) to 49 of 54 (91%). The percentage of awardees meeting the target (80%) for associated clinical laboratories with staff certifications to package/ship rose from 32% (19 of 60) to 46% (25 of 54). The percentage of awardees meeting the target (70%) for associated clinical laboratories with risk assessment policies increased from 18% (8 of 44) to 28% (15 of 54). Awardees reported improvement among Ebola treatment centers/Ebola assessment hospitals with policies to perform risk assessments from 48% (20 of 42) to 67% (34 of 51). Public health laboratories and their clinical partners made progress on their abilities to address biosafety concerns and implement consistent biosafety practices, improving their ability to work safely with biological threats. More attention is needed to address gaps in the clinical community. Support for biosafety activities is critical to continuing to achieve progress.

Public health laboratories (PHLs) provide essential services in the diagnosis and surveillance of diseases of public health concern, such as tuberculosis. Maintaining access to high-quality laboratory testing is critical to continued disease detection and decline of tuberculosis cases in the United States. We investigated the practical experience of sharing tuberculosis testing services between PHLs through the Shared Services Project.
The Shared Services Project was a 9-month-long project funded through the Association of Public Health Laboratories and the Centers for Disease Control and Prevention during 2012-2013 as a one-time funding opportunity to consortiums of PHLs that proposed collaborative approaches to sharing tuberculosis laboratory services. Submitting PHLs maintained testing while simultaneously sending specimens to reference laboratories to compare turnaround times.
During the 9-month project period, 107 Mycobacterium tuberculosis complex submissions for growth-based drug susceptibility testing and molecular detection of drug resistance testing occurred among the 3 consortiums. The median transit time for all submissions was 1.0 day. Overall, median drug susceptibility testing turnaround time (date of receipt in submitting laboratory to result) for parallel testing performed in house by submitting laboratories was 31.0 days; it was 43.0 days for reference laboratories. The median turnaround time for molecular detection of drug resistance results was 1.0 day (mean = 2.8; range, 0-14) from specimen receipt at the reference laboratories.
The shared services model holds promise for specialized tuberculosis testing. Sharing of services requires a balance among quality, timeliness, efficiency, communication, and fiscal costs.