Explore the vast range of titles available.

AbstractObjectiveTo directly measure the fatal impact of coronavirus disease 2019 (covid-19) in an urban African population.DesignProspective systematic postmortem surveillance study.SettingZambia’s largest tertiary care referral hospital.ParticipantsDeceased people of all ages at the University Teaching Hospital morgue in Lusaka, Zambia, enrolled within 48 hours of death.Main outcome measurePostmortem nasopharyngeal swabs were tested via reverse transcriptase quantitative polymerase chain reaction (PCR) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Deaths were stratified by covis-19 status, location, age, sex, and underlying risk factors.Results372 participants were enrolled between June and September 2020; PCR results were available for 364 (97.8%). SARS-CoV-2 was detected in 58/364 (15.9%) according to the recommended cycle threshold value of <40 and in 70/364 (19.2%) when expanded to any level of PCR detection. The median age at death among people with a positive test for SARS-CoV-2 was 48 (interquartile range 36-72) years, and 69% (n=48) were male. Most deaths in people with covid-19 (51/70; 73%) occurred in the community; none had been tested for SARS-CoV-2 before death. Among the 19/70 people who died in hospital, six were tested before death. Among the 52/70 people with data on symptoms, 44/52 had typical symptoms of covid-19 (cough, fever, shortness of breath), of whom only five were tested before death. Covid-19 was identified in seven children, only one of whom had been tested before death. The proportion of deaths with covid-19 increased with age, but 76% (n=53) of people who died were aged under 60 years. The five most common comorbidities among people who died with covid-19 were tuberculosis (22; 31%), hypertension (19; 27%), HIV/AIDS (16; 23%), alcohol misuse (12; 17%), and diabetes (9; 13%).ConclusionsContrary to expectations, deaths with covid-19 were common in Lusaka. Most occurred in the community, where testing capacity is lacking. However, few people who died at facilities were tested, despite presenting with typical symptoms of covid-19. Therefore, cases of covid-19 were under-reported because testing was rarely done not because covid-19 was rare. If these data are generalizable, the impact of covid-19 in Africa has been vastly underestimated.

Antimicrobial resistance (AMR) is a public health problem threatening human, animal, and environmental safety. This study assessed the AMR profiles and risk factors associated with Escherichia coli in hospital and environmental settings in Lusaka, Zambia. This cross-sectional study was conducted from April 2022 to August 2022 using 980 samples collected from clinical and environmental settings. Antimicrobial susceptibility testing was conducted using BD PhoenixTM 100. The data were analysed using SPSS version 26.0. Of the 980 samples, 51% were from environmental sources. Overall, 64.5% of the samples tested positive for E. coli, of which 52.5% were from clinical sources. Additionally, 31.8% were ESBL, of which 70.1% were clinical isolates. Of the 632 isolates, 48.3% were MDR. Most clinical isolates were resistant to ampicillin (83.4%), sulfamethoxazole/trimethoprim (73.8%), and ciprofloxacin (65.7%) while all environmental isolates were resistant to sulfamethoxazole/trimethoprim (100%) and some were resistant to levofloxacin (30.6%). The drivers of MDR in the tested isolates included pus (AOR = 4.6, CI: 1.9–11.3), male sex (AOR = 2.1, CI: 1.2–3.9), and water (AOR = 2.6, CI: 1.2–5.8). This study found that E. coli isolates were resistant to common antibiotics used in humans. The presence of MDR isolates is a public health concern and calls for vigorous infection prevention measures and surveillance to reduce AMR and its burdens.

ObjectivesTo determine the prevalence of COVID-19 postmortem setting in Lusaka, Zambia.DesignA systematic, postmortem prevalence study.SettingA busy, inner-city morgue in Lusaka.ParticipantsWe sampled a random subset of all decedents who transited the University Teaching Hospital morgue. We sampled the posterior nasopharynx of decedents using quantitative PCR. Prevalence was weighted to account for age-specific enrolment strategies.InterventionsNot applicable—this was an observational study.Primary outcomesPrevalence of COVID-19 detections by PCR. Results were stratified by setting (facility vs community deaths), age, demographics and geography and time.Secondary outcomesShifts in viral variants; causal inferences based on cycle threshold values and other features; antemortem testing rates.ResultsFrom 1118 decedents enrolled between January and June 2021, COVID-19 was detected among 32.0% (358/1116). Roughly four COVID-19+ community deaths occurred for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths and overall, only ~10% of COVID-19+ deaths were identified in life. During peak transmission periods, COVID-19 was detected in ~90% of all deaths. We observed three waves of transmission that peaked in July 2020, January 2021 and ~June 2021: the AE.1 lineage and the Beta and Delta variants, respectively. PCR signals were strongest among those whose deaths were deemed ‘probably due to COVID-19’, and weakest among children, with an age-dependent increase in PCR signal intensity.ConclusionsCOVID-19 was common among deceased individuals in Lusaka. Antemortem testing was rarely done, and almost never for community deaths. Suspicion that COVID-19 was the cause of deaths was highest for those with a respiratory syndrome and lowest for individuals <19 years.

BACKGROUND Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or are a consequence of it, is unknown. In order to answer this question, longitudinal studies are needed. METHODS We conducted a retrospective analysis of NP samples collected in a longitudinal birth cohort study of Zambian mother-infant pairs. Samples were collected every two weeks from 1-week through 14-weeks of age. Ten of the infants in the cohort who developed LRTI were matched 1:3 with healthy comparators. We completed 16S rRNA gene sequencing on the samples each of these infants contributed and compared the NP microbiome of the healthy infants to infants who developed LRTI. RESULTS The infant NP microbiome maturation was characterized by transitioning from Staphylococcus dominant to respiratory-genera dominant profiles during the first three months of life, similar to what is described in the literature. Interestingly, infants who developed LRTI had distinct NP microbiome characteristics before infection, in most cases as early as the first week of life. Their NP microbiome was characterized by the presence of Novosphingobium, Delftia, high relative abundance of Anaerobacillus, Bacillus, and low relative abundance of Dolosigranulum, compared to the healthy controls. Mothers of infants with LRTI also had low relative abundance of Dolosigranulum in their baseline samples compared to mothers of infants that did not develop an LRTI. CONCLUSIONS Our results suggest that specific characteristics of the NP microbiome precede LRTI in young infants and may be present in their mothers as well. Early dysbiosis may play a role in the causal pathway leading to LRTI or could be a marker of underlying immunological, environmental, or genetic characteristics that predispose to LRTI.

East Coast Fever (ECF), caused by Theileria parva, is a major constraint to improved livestock keeping in east and central Africa, including Zambia. To understand the dynamics and determine the candidates for immunization in Zambia’s Chongwe and Chisamba districts, a combination of Tp1 and Tp2 gene sequencing and microsatellite analysis using nine markers was conducted from which an abundance of Muguga, Kiambu, Serengeti and Katete epitopes in the field samples was obtained. Phylogenetic analysis showed six (Tp1) and three (Tp2) clusters with an absence of geographical origin clustering. The majority of haplotypes were related to Muguga, Kiambu, Serengeti and Katete, and only a few were related to Chitongo. Both antigens showed purifying selection with an absence of positive selection sites. Furthermore, low to moderate genetic differentiation was observed among and within the populations, and when vaccine stocks were compared with field samples, Chongwe samples showed more similarity to Katete and less to Chitongo, while Chisamba samples showed similarity to both Katete and Chitongo and not to Muguga, Kiambu or Serengeti. We conclude that the use of Katete stock for immunization trials in both Chongwe and Chisamba districts might produce desirable protection against ECF.

Antimicrobial resistance (AMR) is a public health problem threatening human, animal, and environmental safety. This study assessed the AMR profiles and risk factors associated with Escherichia coli in hospital and environmental settings in Lusaka, Zambia. This cross-sectional study was conducted from April 2022 to August 2022 using 980 samples collected from clinical and environmental settings. Antimicrobial susceptibility testing was conducted using BD Phoenix[sup.TM] 100. The data were analysed using SPSS version 26.0. Of the 980 samples, 51% were from environmental sources. Overall, 64.5% of the samples tested positive for E. coli, of which 52.5% were from clinical sources. Additionally, 31.8% were ESBL, of which 70.1% were clinical isolates. Of the 632 isolates, 48.3% were MDR. Most clinical isolates were resistant to ampicillin (83.4%), sulfamethoxazole/trimethoprim (73.8%), and ciprofloxacin (65.7%) while all environmental isolates were resistant to sulfamethoxazole/trimethoprim (100%) and some were resistant to levofloxacin (30.6%). The drivers of MDR in the tested isolates included pus (AOR = 4.6, CI: 1.9–11.3), male sex (AOR = 2.1, CI: 1.2–3.9), and water (AOR = 2.6, CI: 1.2–5.8). This study found that E. coli isolates were resistant to common antibiotics used in humans. The presence of MDR isolates is a public health concern and calls for vigorous infection prevention measures and surveillance to reduce AMR and its burdens.