Incorporating COVID-19 into Acute Febrile Illness Surveillance Systems, Belize, Kenya, Ethiopia, Peru, and Liberia, 2020-2021.

Existing acute febrile illness (AFI) surveillance systems can be leveraged to identify and characterize emerging pathogens, such as SARS-CoV-2, which causes COVID-19. The US Centers for Disease Control and Prevention collaborated with ministries of health and implementing partners in Belize, Ethiopia, Kenya, Liberia, and Peru to adapt AFI surveillance systems to generate COVID-19 response information. Staff at sentinel sites collected epidemiologic data from persons meeting AFI criteria and specimens for SARS-CoV-2 testing. A total of 5,501 patients with AFI were enrolled during March 2020-October 2021; >69% underwent SARS-CoV-2 testing. Percentage positivity for SARS-CoV-2 ranged from 4% (87/2,151, Kenya) to 19% (22/115, Ethiopia). We show SARS-CoV-2 testing was successfully integrated into AFI surveillance in 5 low- to middle-income countries to detect COVID-19 within AFI care-seeking populations. AFI surveillance systems can be used to build capacity to detect and respond to both emerging and endemic infectious disease threats.

Burden of Diarrhoeagenic Escherichia coli in Santa Rosa, Guatemala in active health-services surveillance during 2008-2009 and 2014-2015.

OBJECTIVE: To describe the epidemiology of laboratory-confirmed Diarrhoeagenic Escherichia coli (DEC) cases from active facility-based surveillance in Guatemala. METHODS: We collected clinical and risk factor data on enrolled patients (aged 0-52 years) with acute diarrhoea at government healthcare facilities (1 hospital and 6 clinics) in Santa Rosa, Guatemala, during 2008-2009 and 2014-2015. Stool samples were analysed, E. coli identified through culture and biochemical tests, PCR amplification of genes encoding pathotype-specific virulence factors identified specific DEC pathotypes. Healthcare-seeking adjusted incidence rates were calculated. RESULTS: A total of 3041 diarrhoea cases were captured by surveillance (647 hospitalisations (H), 2394 clinic visits (CV)); general E. coli prevalence was 17.9%. DEC pathotypes were identified in 19% (n = 95/497) and 21% (n = 450/2113) in diarrhoea H and CV, respectively. Enteropathogenic E. coli (EPEC) was most frequently isolated (8.2% (n = 41) in diarrhoea H, 12.0% (n = 255) in diarrhoea CV), followed by ETEC (6.8% (n = 34) in H, 6% (n = 128) in CV) and STEC (0.6% (n = 3) in H, 0.6% (n = 13) in CV). We did not find evidence of a difference in severity between DEC and non-DEC diarrhoea. Incidence of DEC clinic visits and hospitalisations was 648.0 and 29.3, respectively, per 10,000 persons aged ≤5 years and 36.8 and 0.4, respectively, per 10,000 persons aged >5 years. CONCLUSIONS: DEC pathotypes, especially EPEC and ETEC, were detected frequently from patients presenting with diarrhoeal illness in Santa Rosa, Guatemala. Our findings suggest that preventive interventions should be prioritised for young children.

Hospitalization and death among patients with influenza, Guatemala, 2008-2012.

BACKGROUND: Influenza is a major cause of respiratory illness resulting in 3-5 million severe cases and 291,243-645,832 deaths annually. Substantial health and financial burden may be averted by annual influenza vaccine application, especially for high risk groups. METHODS: We used an active facility-based surveillance platform for acute respiratory diseases in three hospitals in Guatemala, Central America, to estimate the incidence of laboratory-confirmed hospitalized influenza cases and identify risk factors associated with severe disease (defined as admission to the intensive care unit (ICU) or death). We enrolled patients presenting with signs and symptoms of acute respiratory infection (ARI) and obtained naso- and oropharyngeal samples for real-time reverse transcriptase polymerase chain reaction (RT-PCR). We used multivariable logistic regression to identify risk factors for ICU admission or death, adjusted for age and sex. RESULTS: From May 2008 to July 2012, among 6326 hospitalized ARI cases, 446 (7%) were positive for influenza: of those, 362 (81%) had influenza A and 84 (18%) had influenza B. Fifty nine percent of patients were aged ≤ 5 years, and 10% were aged ≥ 65 years. The median length of hospitalization was 5 days (interquartile range: 5). Eighty of 446 (18%) were admitted to the ICU and 28 (6%) died. Among the 28 deaths, 7% were aged ≤ 6 months, 39% 7-60 months, 21% 5-50 years, and 32% ≥ 50 years. Children aged ≤ 6 months comprised 19% of cases and 22% of ICU admissions. Women of child-bearing age comprised 6% of cases (2 admitted to ICU; 1 death). In multivariable analyses, Santa Rosa site (adjusted odds ratio [aOR] = 10, 95% confidence interval [CI] = 2-50), indigenous ethnicity (aOR = 4, 95% CI = 2-13, and radiologically-confirmed pneumonia (aOR = 5, 95% CI = 3-11) were independently associated with severe disease. Adjusted for hospital utilization rate, annual incidence of hospitalized laboratory-confirmed influenza was 24/100,000 overall, 93/100,000 for children aged < 5 years and 50/100,000 for those ≥ 65 years. CONCLUSIONS: Influenza is a major contributor of hospitalization and death due to respiratory diseases in Guatemala. Further application of proven influenza prevention and treatment strategies is warranted.

Bartonella vinsonii subsp. arupensis in humans, Thailand.

We identified Bartonella vinsonii subsp. arupensis in pre-enriched blood of 4 patients from Thailand. Nucleotide sequences for transfer-messenger RNA gene, citrate synthase gene, and the 16S-23S rRNA internal transcribed spacer were identical or closely related to those for the strain that has been considered pathogenic since initially isolated from a human in Wyoming, USA.

A Multilingual Tool for Standardized Laboratory Biosafety and Biosecurity Assessment and Monitoring.

Control of infectious diseases requires the handling of infectious materials by both clinical and public health laboratories with exposure risks for laboratory personnel and environment. A comprehensive tool for assessing the capacity to manage these risks could enable the development of action plans for mitigation. Under the framework of the Global Health Security Agenda action package for biosafety and biosecurity, the authors developed a tool dedicated to assessing laboratory biosafety and biosecurity. The Biosafety and Biosecurity Laboratory Assessment Tool (BSS LAT) assesses the status of all laboratory biosafety core requirements across 10 different modules. It consists of a standardized spreadsheet-based tool that provides automatic scoring. It is designed to support national, regional, and global efforts to strengthen biosafety in clinical, public health, and veterinary laboratories. The BSS LAT was first used in Burkina Faso in collaboration with the African Society for Laboratory Medicine and the US Centers for Disease Control and Prevention to support the country in strengthening their biorisk management system. Since then, it has been successfully used in other countries (ie, Armenia, Burundi, Cameroon, Ghana, Guinea, Kazakhstan, Liberia), various settings (medical and veterinary laboratories), and translated into several languages (eg, English, French, Russian). The BSS LAT is a multipurpose tool that assists with standardization of biosafety and biosecurity requirements for all laboratories working with infectious materials, serves as a self-assessment guide for laboratories to develop improvement plans and reinforce capacities, and serves as a training guide for individual laboratories and networks or at the national level. The BSS LAT can also be used as a monitoring tool for the assessment of biosafety and biosecurity across all laboratories working with infectious materials at the national, regional, and global levels.

Strengthening laboratory biosafety in Liberia during the COVID-19 pandemic: Experience from the Global Laboratory Leadership Programme.

Background: The Global Laboratory Leadership Programme (GLLP) has biosafety and biosecurity as one of its core competencies and advocates for a One Health approach involving all relevant sectors across the human-animal-environment interface to empower national laboratory systems and strengthen health security. Decentralization of SARS-CoV-2 testing in Liberia coupled with an increase in the number of COVID-19 infections among laboratory professionals raised biosafety concerns. In response, a set of trainings on laboratory biosafety was launched for lab personnel across the country under the framework of the GLLP. The goal was to deliver a comprehensive package for laboratory biosafety in the context of SARS-CoV-2 through active learning. Methods: Three one-day workshops were conducted between September and October 2020, training personnel from human, animal and environmental laboratories through a One Health approach. Concepts critical to laboratory biosafety were delivered in an interactive engagement format to ensure effective learning and retention of concepts. Pre- and post-training assessments were performed, and a paired t-test was used to assess knowledge gain. Results: Of the 67 participants, 64 were from the human health sector, one from veterinary sector and two from environmental health sector. The average pre-test score was 41%. The main gaps identified were failure to acknowledge surgical antisepsis as a form of hand hygiene and recognition of PPE as the best risk control measure. The average post-test score was 75.5%. The mean difference of pre-test and post-test scores was statistically significant (p-value <0.001). Participants indicated satisfaction with the workshop content, mode of delivery and trainers' proficiency. Conclusions: The workshops were impactful as evidenced by significant improvement (34.5%) in the post-test scores and positive participant feedback. Repeated refresher trainings are vital to addressing the gaps, ensuring compliance, and promoting biosafety culture. GLLP's approach to cultivating multisectoral national laboratory leaders ready to take responsibility and ownership for capacity building provides a sustainable solution for attaining strong national laboratory systems better prepared for health emergencies and pandemics like COVID-19.

Bartonella seroprevalence in rural Thailand.

We estimated the prevalence of anti-Bartonella antibodies among febrile and non-febrile patients presenting to community hospitals in rural Thailand from February 2002 through March 2003. Single serum specimens were tested for IgG titers to four Bartonella species, B. henselae, B. quintana, B. elizabethae and B. vinsonii subsp vinsonii using an indirect immunofluorescent assay. A titer 21:256 was considered positive. Forty-two febrile patients (9.9%) and 19 non-febrile patients (19%) had positive serology titers to at least one Bartonella species. Age-standardized Bartonella seroprevalence differed significantly between febrile (10%) and non-febrile patients (18%, p=0.047), but did not differ by gender. Among all 521 patients, IgG titers 21:256 to B. henselae were found in 20 participants (3.8%), while 17 (3.3%) had seropositivity to B. quintana, 51 (9.8%) to B. elizabethae, and 19 (3.6%) to B. vinsonii subsp vinsonii. These results suggest exposure to Bartonella species is more common in rural Thailand than previously suspected.

National Biosafety Management System: A Combined Framework Approach Based on 15 Key Elements.

The pervasive nature of infections causing major outbreaks have elevated biosafety and biosecurity as a fundamental component for resilient national laboratory systems. In response to international health security demands, the Global Health Security Agenda emphasizes biosafety as one of the prerequisites to respond effectively to infectious disease threats. However, biosafety management systems (BMS) in low-medium income countries (LMIC) remain weak due to fragmented implementation strategies. In addition, inefficiencies in implementation have been due to limited resources, inadequate technical expertise, high equipment costs, and insufficient political will. Here we propose an approach to developing a strong, self-sustaining BMS based on extensive experience in LMICs. A conceptual framework incorporating 15 key components to guide implementers, national laboratory leaders, global health security experts in building a BMS is presented. This conceptual framework provides a holistic and logical approach to the development of a BMS with all critical elements. It includes a flexible planning matrix with timelines easily adaptable to different country contexts as examples, as well as resources that are critical for developing sustainable technical expertise.

Incidence of pneumococcal bacteremia requiring hospitalization in rural Thailand.

BACKGROUND: Population-based estimates of the incidence of invasive pneumococcal disease are unavailable for Thailand and other countries in Southeast Asia. We estimated the incidence of pneumococcal bacteremia cases requiring hospitalization in rural Thailand. METHODS: Blood cultures were performed on samples from hospitalized patients in 2 rural provinces where active, population-based surveillance of community-acquired pneumonia is conducted. Blood cultures were performed at clinician discretion and were encouraged for all patients with suspected pneumonia and all children aged <5 years with suspected sepsis. Pneumococcal antigen testing was performed on positive blood culture specimens that failed to grow organisms on subculture. RESULTS: From May 2005 through June 2007, 23,853 blood culture specimens were collected overall, and 7319 were collected from children aged <5 years, which represented 66% and 47% of target patients, respectively. A total of 72 culture-confirmed pneumococcal bacteremia cases requiring hospitalization were identified. An additional 44 patients had media from positive blood cultures that yielded no growth on subculture but that had positive results of pneumococcal antigen testing. Of the 116 confirmed cases of bacteremia, 27 (23%) occurred in children aged <5 years; of these, 9 (33%) were confirmed by antigen testing only. The incidence of pneumococcal bacteremia cases requiring hospitalization among children aged <5 years had a range of 10.6-28.9 cases per 100,000 persons (incidence range if cases detected by antigen are excluded, 7.5-14.0 cases per 100,000 persons). CONCLUSIONS: Invasive pneumococcal disease is more common than was previously suspected in Thailand, even on the basis of estimates limited to hospitalized cases of bacteremia. These estimates, which are close to estimates of the incidence of hospitalized cases of pneumococcal bacteremia in the United States before introduction of pneumococcal conjugate vaccine, provide important data to guide public health care policy and to inform discussions about vaccine introduction in Thailand and the rest of Southeast Asia.

Bartonella tamiae sp. nov., a newly recognized pathogen isolated from three human patients from Thailand.

Three strains of a novel Bartonella species (Bartonella tamiae) were isolated from human patients from Thailand. Sequence analysis of six chromosomal regions (16S rRNA, gltA, groEL, ftsZ, rpoB, and the intergenic spacer region) and phenotypical analysis supported the similarity of the three strains and placed them within the genus Bartonella separately from previously described species.

Field Epidemiology and Laboratory Training Program, Where Is the L-Track?

Background: Modifications of the Field Epidemiology Training Program (FETP) curricula to include a laboratory track (L-Track), to become Field Epidemiology and Laboratory Training Program (FELTP), began in 2004 in Kenya. The L-Track offered candidates training on laboratory competencies in management, policy, quality systems, and diagnostic methods as well as epidemiology, disease surveillance and outbreak response. Since then several FELTPs have discontinued the L-Track and instead offer all candidates, epidemiologists and laboratorians, a single FETP curriculum. Reasons for these changes are reported here. Methods: A questionnaire was sent to directors of 13 FELTP programs collecting information on the status of the programs, reasons for any changes, basic entry qualifications, source institutions and where residents were post enrollment or after graduation. Data from previous CDC internal assessments on FELTP L-Track was also reviewed. Results: Out of the 13 FELTPs included, directors from 10 FELTPs sent back information on their specific programs. The FELTPs in Kenya, Mozambique, Cameroon and Kazakhstan and Mali have discontinued a separate L-Track while those in Ghana, Georgia, Nigeria, Rwanda, and Tanzania continue to offer the separate L-Track. Reasons for discontinuation included lack of standardized curriculum, unclear strategies of the separate L-Track, and funding constraints. Two countries Kenya and Tanzania reported on the career progression of their graduates. Results show 84% (Kenya) and 51% (Tanzania) of candidates in the FELTP, L-Track were recruited from national/regional medical health laboratories. However post-graduation, 56% (Kenya) and 43% (Tanzania) were working as epidemiologists, program managers, program coordinators, or regulatory/inspection boards. Professional upward mobility was high; 87% (Kenya) and 73% (Tanzania) residents, reported promotions either in the same or in new institutions. Conclusions: The FELTP L-Track residents continue to offer critical contributions to public health workforce development with high upward mobility. While this may be a reflection of professional versatility and demand of the FELTP graduates, the move from core laboratory services underscores the challenges in filling and retaining qualified staff within the laboratory systems. Results suggest different strategies are needed to strengthen laboratory management and leadership programs with a clear focus on laboratory systems and laboratory networks to meet current and future clinical and public health laboratory workforce demands.

Outbreak Investigation of Plasmodium vivax Malaria in a Region of Guatemala Targeted for Malaria Elimination.

AbstractThe Department of Santa Rosa, Guatemala, is targeted for malaria elimination. However, compared with 2011, a 13-fold increase in cases was reported in 2012. To describe the epidemiology of malaria in Santa Rosa in the setting of the apparent outbreak, demographic and microscopic data from 2008 to 2013 were analyzed. In April 2012, a new surveillance strategy, funded by the Global Fund to Fight AIDS, Tuberculosis and Malaria, was introduced involving more active case detection, centralized microscopy, increased community engagement, and expanded vector control. Interviews with vector control personnel and site visits were conducted in June 2013. From 2008 to 2013, 337 cases of malaria were reported. The increase in cases occurred largely after the new surveillance strategy was implemented. Most (137/165; 83%) 2012 cases came from one town near a lake. Plasmodium vivax was the malaria species detected in all cases. Cases were detected where malaria was not previously reported. Monthly rainfall or/and temperature did not correlate with cases. Interviews with public health personnel suggested that the new funding, staffing, and strategy were responsible for improved quality of malaria detection and control and thus the increase in reported cases. Improvements in surveillance, case detection, and funding appear responsible for the temporary increase in cases, which thus may paradoxically indicate progress toward elimination.

Diversity and phylogenetic relationships among Bartonella strains from Thai bats.

Bartonellae are phylogenetically diverse, intracellular bacteria commonly found in mammals. Previous studies have demonstrated that bats have a high prevalence and diversity of Bartonella infections globally. Isolates (n = 42) were obtained from five bat species in four provinces of Thailand and analyzed using sequences of the citrate synthase gene (gltA). Sequences clustered into seven distinct genogroups; four of these genogroups displayed similarity with Bartonella spp. sequences from other bats in Southeast Asia, Africa, and Eastern Europe. Thirty of the isolates representing these seven genogroups were further characterized by sequencing four additional loci (ftsZ, nuoG, rpoB, and ITS) to clarify their evolutionary relationships with other Bartonella species and to assess patterns of diversity among strains. Among the seven genogroups, there were differences in the number of sequence variants, ranging from 1-5, and the amount of nucleotide divergence, ranging from 0.035-3.9%. Overall, these seven genogroups meet the criteria for distinction as novel Bartonella species, with sequence divergence among genogroups ranging from 6.4-15.8%. Evidence of intra- and intercontinental phylogenetic relationships and instances of homologous recombination among Bartonella genogroups in related bat species were found in Thai bats.

Enterotoxigenic Escherichia coli colonization factor types collected from 1997 to 2001 in US military personnel during operation Bright Star in northern Egypt.

Operation Bright Star (OBS) is a biennial, multinational exercise in Egypt involving 15000 US troops. Consistent with past observations in deployed troops, diarrhea is the most significant cause of morbidity. Focused efforts are ongoing to develop vaccines against the most common pathogens affecting our troops. As part of these efforts, diarrhea surveillance was conducted during OBS to monitor pathogens associated with illness and to identify new vaccine targets. A retrospective review was conducted of prior studies with similar methods. Soldiers with diarrhea presenting to the OBS clinic provided a stool sample that was inoculated into Carey-Blair transport media. Within 3 days, the Cary-Blair tubes were transported to the Naval Medical Research Unit no. 3 in Cairo where bacterial culture was performed. As part of the evaluation, 5 Escherichia coli-like colonies were collected and tested for toxin production using the GM1-ELISA. Toxin-positive isolates were further tested for colonization factors (CF) by a dot-blot assay using a standardized panel of monoclonal antibodies against CFA/I, CS1-CS7, CS17, CS8 (CFA/III), CS12 (PCFO159), and CS14 (PCFO166). Enterotoxigenic E. coli (ETEC) was the most frequently isolated pathogen during each OBS from which data were collected. The rate of ETEC-associated diarrhea ranged from 22% to 58%. Over time, there were dramatic shifts in the frequency and distribution of CFs. Over the 5 years of study, an increasing number of ETEC isolates had no known CF identified, and in 2001, only 40% of ETEC was associated with known CFs. The most commonly identified CF was CS6. Diarrheal disease, particularly ETEC, continues to be a common malady among US military personnel deployed to Egypt. We have identified ETEC CF types, especially CS6, which should be considered potential vaccine candidates. However, despite intensive testing, CFs could not be identified in most of the ETEC isolated, highlighting the need for further studies to identify novel CFs and alternative vaccine targets.

Coexistence of Bartonella henselae and B. clarridgeiae in populations of cats and their fleas in Guatemala.

Cats and their fleas collected in Guatemala were investigated for the presence of Bartonella infections. Bartonella bacteria were cultured from 8.2% (13/159) of cats, and all cultures were identified as B. henselae. Molecular analysis allowed detection of Bartonella DNA in 33.8% (48/142) of cats and in 22.4% (34/152) of cat fleas using gltA, nuoG, and 16S-23S internal transcribed spacer targets. Two Bartonella species, B. henselae and B. clarridgeiae, were identified in cats and cat fleas by molecular analysis, with B. henselae being more common than B. clarridgeiae in the cats (68.1%; 32/47 vs 31.9%; 15/47). The nuoG was found to be less sensitive for detecting B. clarridgeiae compared with other molecular targets and could detect only two of the 15 B. clarridgeiae-infected cats. No significant differences were observed for prevalence between male and female cats and between different age groups. No evident association was observed between the presence of Bartonella species in cats and in their fleas.

First imported Plasmodium ovale malaria in Central America: case report of a Guatemalan soldier and a call to improve its accurate diagnosis.

The Mesoamerican Ministers of Health have set 2020 as the target for malaria elimination to be achieved in the region. Imported malaria cases are a potential threat to countries attempting elimination or working to prevent resurgence. We report the first imported Plasmodium ovale infection with molecular confirmation in Central America, which occurred in a Guatemalan soldier that had been deployed in Africa. The obstacles for its diagnosis using the standard microscopy technique and the need to improve its detection are discussed.

Rapid diagnostic assays in the genomic biology era: detection and identification of infectious disease and biological weapon agents.

In this special section of BioTechniques, we examine the role of rapid molecular technologies in the detection and identification of agents of infectious disease (ID) and biological weapons (BWs). Besides the threat posed by the global proliferation of BW technologies, there are numerous emerging and reemerging ID agents with significant public health consequences. Further compounding this already complicated situation are the estimated 600 million international tourists annually, many with the potential to the spread disease globally in a matter of hours. While clinical laboratories have key roles in the detection and identification of potential ID/BW agents, most staff are unfamiliar with these agents because of their rarity and the often laborious conventional methodologies needed to identify them. To meet this challenge, a vast array of rapid assay strategies has been developed for use in clinical diagnostics and environmental detection. Technologies have been developed or adapted to the challenges posed by these agents, permitting detection and identification in several minutes to hours. In particular, the development of improved reagents and detection systems has led to dramatic improvements in the sensitivity and specificity of immunological and nucleic acid-based systems, allowing an ever-increasing range of analytes to be identified and quantitated. In the accompanying articles, we have brought together experts from the many overlapping aspects of this arena in order to present a comprehensive and critical analysis of these technologies.

Immunoassay of infectious agents.

Immunoassays have evolved for a broad range of applications since the pioneering work of Yalow and Berson who developed the first competitive radioimmunoassay (RIA) for human insulin in 1959. Immunoassay detection of specific antigens and host-produced antibodies directed against such antigens consitutes one of the most widely used and successful methods for diagnosing infectious diseases (IDs). The number and variety of new assay systems that are continually being developed reflect the increasing demand for immunoassays possessing greater sensitivity, speed, and ease of use. This trend has been driven, in part, by the need for improved immunodiagnostic systems to perform rapid testing and counter emerging IDs and biothreat (BT) agents. Another factor driving this trend is the need to integrate immunoassays with more sensitive nucleic acid-based methods for a comprehensive approach. Here we examine the development of immunoassays, some of the key formats used for the detection and identification of BT/ID agents, and the application of these technologies under different scenarios.