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Giardia duodenalis (syn. G. intestinalis, G. lamblia) is a widespread gastrointestinal protozoan parasite with debated taxonomic status. Currently, eight distinct genetic sub-groups, termed assemblages A-H, are defined based on a few genetic markers. Assemblages A and B may represent distinct species and are both of human public health relevance. Genomic studies are scarce and the few reference genomes available, in particular for assemblage B, are insufficient for adequate comparative genomics. Here, by combining long- and short-read sequences generated by PacBio and Illumina sequencing technologies, we provide nine annotated genome sequences for reference from new clinical isolates (four assemblage A and five assemblage B parasite isolates). Isolates chosen represent the currently accepted classification of sub-assemblages AI, AII, BIII and BIV. Synteny over the whole genome was generally high, but we report chromosome-level translocations as a feature that distinguishes assemblage A from B parasites. Orthologue gene group analysis was used to define gene content differences between assemblage A and B and to contribute a gene-set-based operational definition of respective taxonomic units. Giardia is tetraploid, and high allelic sequence heterogeneity (ASH) for assemblage B vs. assemblage A has been observed so far. Noteworthy, here we report an extremely low ASH (0.002%) for one of the assemblage B isolates (a value even lower than the reference assemblage A isolate WB-C6). This challenges the view of low ASH being a notable feature that distinguishes assemblage A from B parasites, and low ASH allowed assembly of the most contiguous assemblage B genome currently available for reference. In conclusion, the description of nine highly contiguous genome assemblies of new isolates of G. duodenalis assemblage A and B adds to our understanding of the genomics and species population structure of this widespread zoonotic parasite.

North-South educational partnerships can potentially alleviate the scarcity of health work force in the South. A model program with the objectives of sustainability, high trainee retention, quality education, and capacity building is the goal of many similar programs. To achieve these goals a program of postgraduate clinical specialty training was implemented, between the University of Bergen, Norway and three Universities in Africa and one medical school in India between 2008 to 2014. This partnership program aimed at educating physicians from the South to specialize in various medical field. The goal was that the trained physicians would be educators in their respective countries. The program participants were 58 medical doctors. At the end of the program we conducted an evaluation survey involving program participants and coordinators. Twenty-eight physicians (48%) responded to the survey. The average program evaluation score by the physicians was 4.5 (out of a maximum of 5) with a range of 3.2 to 5. Out of the 12 program coordinators 9 (75%) responded to the survey. Their average score was 4.5 with a range of 4 to 4.9. By the time the survey was conducted, 49 of the 58 (84.5%) program participants had completed the program successfully and 47 of the 49 (95.9%) were working in their own countries. In conclusion, the partnership program was effective in capacity building in the development of the human health workforce in Africa. We have observed a high retention rate, good quality education, a sustainable program and the model can easily be reproducible.

Giardia lamblia, one of the most common protozoal infections of the human intestine, is an important worldwide cause of diarrheal disease, malabsorption, malnutrition, delayed cognitive development in children, and protracted postinfectious syndromes. Despite its medical importance, no human vaccine is available against giardiasis. A crude veterinary vaccine has been developed, and experimental vaccines based on expression of multiple variant-specific surface proteins have been reported, but poorly defined vaccine components and excessive antigen variability are problematic for pharmaceutical vaccine production. To expand the repertoire of antigen candidates for vaccines, we reasoned that surface proteins may provide an enriched source of such antigens since key host effectors, such as secretory IgA, can directly bind to such antigens in the intestinal lumen and interfere with epithelial attachment. Here, we have applied a proteomics approach to identify 23 novel surface antigens of G. lamblia that show >90% amino acid sequence identity between the two human-pathogenic genetic assemblages (A and B) of the parasite. Surface localization of a representative subset of these proteins was confirmed by immunostaining. Four selected proteins, uridine phosphorylase-like protein-1, protein 21.1 (GL50803_27925), α1-giardin, and α11-giardin, were subsequently produced in recombinant form and shown to be immunogenic in mice and G. lamblia-infected humans and confer protection against G. lamblia infection upon intranasal immunization in rodent models of giardiasis. These results demonstrate that identification of conserved surface antigens provides a powerful approach for overcoming a key rate-limiting step in the design and construction of an effective vaccine against giardiasis.

Background: Typhoid fever is a common cause of febrile illness in low- and middle-income countries. While multidrug-resistant (MDR) Salmonella Typhi (S. Typhi) has spread globally, fluoroquinolone resistance has mainly affected Asia. Methods: Consecutively, 1038 blood cultures were obtained from patients of all age groups with fever and/or suspicion of serious systemic infection admitted at Mnazi Mmoja Hospital, Zanzibar in 2015–2016. S. Typhi were analyzed with antimicrobial susceptibility testing and with short read (61 strains) and long read (9 strains) whole genome sequencing, including three S. Typhi strains isolated in a pilot study 2012–2013. Results: Sixty-three S. Typhi isolates (98%) were MDR carrying blaTEM-1B, sul1 and sul2, dfrA7 and catA1 genes. Low-level ciprofloxacin resistance was detected in 69% (43/62), with a single gyrase mutation gyrA-D87G in 41 strains, and a single gyrA-S83F mutation in the non-MDR strain. All isolates were susceptible to ceftriaxone and azithromycin. All MDR isolates belonged to genotype 4.3.1 lineage I (4.3.1.1), with the antimicrobial resistance determinants located on a composite transposon integrated into the chromosome. Phylogenetically, the MDR subgroup with ciprofloxacin resistance clusters together with two external isolates. Conclusions: We report a high rate of MDR and low-level ciprofloxacin resistant S. Typhi circulating in Zanzibar, belonging to genotype 4.3.1.1, which is widespread in Southeast Asia and African countries and associated with low-level ciprofloxacin resistance. Few therapeutic options are available for treatment of typhoid fever in the study setting. Surveillance of the prevalence, spread and antimicrobial susceptibility of S. Typhi can guide treatment and control efforts. Author summary: Salmonella Typhi causes typhoid fever. Multi-drug resistant (MDR) S. Typhi is spreading globally. Local and regional surveillance of MDR S. Typhi populations using both blood culture and whole genome sequencing can uncover outbreaks and help mapping the spread of S. Typhi and resistance mechanisms, which, in turn, can guide both control and prevention efforts and clinical management. Data regarding the distribution of MDR S. Typhi genotypes and resistance mechanisms is scarce in Zanzibar, Tanzania, as in many other African countries. In this study we characterize S. Typhi phenotypically and genotypically. This study shows high rate of MDR S. Typhi, hence few therapeutic options are available for treatment of typhoid fever in the study setting. Our findings contribute to the knowledge base on typhoid fever in the region and to guide correct treatment of individual patients and control of the disease. [ABSTRACT FROM AUTHOR]

Obesity is a known risk factor for severe respiratory tract infections. In this prospective study, we assessed the impact of being obese or overweight on longitudinal SARS-CoV-2 humoral and cellular responses up to 18 months after infection. 274 patients provided blood samples at regular time intervals up to 18 months including obese (BMI ≥30, n=32), overweight (BMI 25-29.9, n=103) and normal body weight (BMI 18.5-24.9, n=134) SARS-CoV-2 patients. We determined SARS-CoV-2 spike-specific IgG, IgA, IgM levels by ELISA and neutralising antibody titres by neutralisation assay. RBD- and spike-specific memory B cells were investigated by ELISpot, spike- and non-spike-specific IFN-g, IL-2 and IFN-g/IL-2 secreting T cells by FluoroSpot and T cell receptor (TCR) sequencing was performed. Higher BMI correlated with increased COVID-19 severity. Humoral and cellular responses were stronger in overweight and obese patients than normal weight patients and associated with higher spike-specific IgG binding titres relative to neutralising antibody titres. Linear regression models demonstrated that BMI, age and COVID-19 severity correlated independently with higher SARS-CoV-2 immune responses. We found an increased proportion of unique SARS-CoV-2 specific T cell clonotypes after infection in overweight and obese patients. COVID-19 vaccination boosted humoral and cellular responses irrespective of BMI, although stronger immune boosting was observed in normal weight patients. Overall, our results highlight more severe disease and an overreactivity of the immune system in overweight and obese patients after SARSCoV-2 infection, underscoring the importance of recognizing overweight/obese individuals as a risk group for prioritisation for COVID-19 vaccination. [ABSTRACT FROM AUTHOR]

Background Acute undifferentiated fever (AUF) ranges from self-limiting illness to life-threatening infections, such as sepsis, malaria, dengue, leptospirosis and rickettsioses. Similar clinical presentation challenges the clinical management. This study describes risk factors for death in patients hospitalized with AUF in India. Methods Patients aged ≥5 y admitted with fever for 2–14 d without localizing signs were included in a prospective observational study at seven hospitals in India during 2011–2012. Predictors identified by univariate analysis were analyzed by multivariate logistic regression for survival analysis. Results Mortality was 2.4% (37/1521) and 46.9% (15/32) died within 2 d. History of heart disease (p=0.013), steroid use (p=0.011), altered consciousness (p<0.0001), bleeding (p<0.0001), oliguria (p=0.020) and breathlessness (p=0.015) were predictors of death, as were reduced Glasgow coma score (p=0.005), low urinary output (p=0.004), abnormal breathing (p=0.006), abdominal tenderness (p=0.023), leucocytosis (p<0.0001) and thrombocytopenia (p=0.001) at admission. Etiology was identified in 48.6% (18/37) of fatal cases. Conclusions Bleeding, cerebral dysfunction, respiratory failure and oliguria at admission, suggestive of severe organ failure secondary to systemic infection, were predictors of death. Almost half of the patients who died, died shortly after admission, which, together with organ failure, suggests that delay in hospitalization and, consequently, delayed treatment, contribute to death from AUF. [ABSTRACT FROM AUTHOR]

Background The burden and duration of persistent symptoms after nonsevere coronavirus disease 2019 (COVID-19) remains uncertain. This study aimed to assess postinfection symptom trajectories in home-isolated COVID-19 cases compared with age- and time- matched seronegative controls, and investigate immunological correlates of long COVID. Methods A prospective case-control study included home-isolated COVID-19 cases between February 28 and April 4, 2020, and followed for 12 (n = 233) to 18 (n = 149) months, and 189 age-matched severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-naive controls. We collected clinical data at baseline, 6, 12, and 18 months postinfection, and blood samples at 2, 4, 6, and 12 months for analysis of SARS-CoV-2-specific humoral and cellular responses. Results Overall, 46% (108/233) had persisting symptoms 12 months after COVID-19. Compared with controls, adult cases had a high risk of fatigue (27% excess risk, sex, and comorbidity adjusted odds ratio [aOR] 5.86; 95% confidence interval [CI], 3.27–10.5), memory problems (21% excess risk; aOR 7.42; CI, 3.51–15.67), concentration problems (20% excess risk; aOR 8.88; 95% CI, 3.88–20.35), and dyspnea (10% excess risk; aOR 2.66; 95% CI, 1.22–5.79). The prevalence of memory problems increased overall from 6 to 18 months (excess risk 11.5%; 95% CI, 1.5–21.5; P =.024) and among women (excess risk 18.7%; 95% CI, 4.4–32.9; P =.010). Longitudinal spike immunoglobulin G was significantly associated with dyspnea at 12 months. The spike-specific clonal CD4+ T-cell receptor β depth was significantly associated with both dyspnea and number of symptoms at 12 months. Conclusions This study documents a high burden of persisting symptoms after mild COVID-19 and suggests that infection induced SARS-CoV-2-specific immune responses may influence long-term symptoms. [ABSTRACT FROM AUTHOR]

Background: Comparative data on COVID-19 among health care workers (HCWs) in different health care settings are scarce. This study investigated the rates of previous COVID-19 among HCWs in nursing homes, hospitals and a municipal emergency room (ER). Methods: We prospectively included 747 HCWs: 313 from nursing homes, 394 from hospitals and 40 from the ER. The diagnosis of COVID-19 was based on serological evidence of SARS-CoV-2 antibody positivity and self-reported RT-PCR positivity prior to inclusion. Information regarding age, sex and exposure to SARS-CoV-2 infection was collected. Results: A total of 4% (11/313) of nursing home HCWs and 6% (28/434) of HCWs in hospitals/the ER tested positive by serology and/or RT-PCR (p = 0.095). Fewer HCWs in nursing homes had occupational exposure to SARS-CoV-2 compared to those in hospitals/the ER (16% vs. 48%, p < 0, 001), but nursing homes had a higher proportion of HCWs with occupational exposure using partial/no PPE (56% vs. 19%, p < 0.001). Nevertheless, no significant differences in the risk for COVID-19 were found in relation to the rate of occupational exposure (p = 0.755) or use of inadequate PPE (p = 0.631). Conclusions: Despite a small sample size, the risk for COVID-19 among HCWs did not appear to be related to the type of health care facility, rates of occupational exposure or use of PPE. [ABSTRACT FROM AUTHOR]

The aim of this study was to evaluate the performances of three commercially available antibody assays for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies at different time points following SARS-CoV-2 infection. Sera from 536 cases, including 207 SARS-CoV-2 PCR positive, were tested for SARS-CoV-2 antibodies with the Wantai receptor binding domain (RBD) total antibody assay, Liaison S1/S2 IgG assay and Alinity i nucleocapsid IgG assay and compared to a two-step reference ELISA (SARS-CoV-2 RBD IgG and SARS-CoV-2 spike IgG). Diagnostic sensitivity, specificity, predictive values and Cohen's kappa were calculated for the commercial assays. The assay's sensitivities varied greatly, from 68.7% to 95.3%, but the specificities remained high (96.9–99.1%). The three tests showed good performances in sera sampled 31 to 60 days after PCR positivity compared to the reference ELISA. The total antibody test performed better than the IgG tests the first 30 days and the nucleocapsid IgG test showed reduced sensitivity two months or more after PCR positivity. Hence, the test performances at different time points should be taken into consideration in clinical practice and epidemiological studies. Spike or RBD IgG tests are preferable in sera sampled more than two months following SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]