Curated and Annotated Dataset of Lung US Images in Zambian Children with Clinical Pneumonia

See also the commentary by Sitek in this issue. Supplemental material is available for this article.

What is the prevalence of COVID-19 detection by PCR among deceased individuals in Lusaka, Zambia? A postmortem surveillance study

OBJECTIVES

To determine the prevalence of COVID-19 postmortem setting in Lusaka, Zambia.

DESIGN

A systematic, postmortem prevalence study.

SETTING

A busy, inner-city morgue in Lusaka.

PARTICIPANTS

We 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.

INTERVENTIONS

Not applicable-this was an observational study.

PRIMARY OUTCOMES

Prevalence of COVID-19 detections by PCR. Results were stratified by setting (facility vs community deaths), age, demographics and geography and time.

SECONDARY OUTCOMES

Shifts in viral variants; causal inferences based on cycle threshold values and other features; antemortem testing rates.

RESULTS

From 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.

CONCLUSIONS

COVID-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.

The impact of ear growth on identification rates using an ear biometric system in young infants

Background Accurate patient identification is essential for delivering longitudinal care. Our team developed an ear biometric system (SEARCH) to improve patient identification. To address how ear growth affects matching rates longitudinally, we constructed an infant cohort, obtaining ear image sets monthly to map a 9-month span of observations. This analysis had three main objectives: 1) map trajectory of ear growth during the first 9 months of life; 2) determine the impact of ear growth on matching accuracy; and 3) explore computer vision techniques to counter a loss of accuracy.   Methodology Infants were enrolled from an urban clinic in Lusaka, Zambia. Roughly half were enrolled at their first vaccination visit and ~half at their last vaccination. Follow-up visits for each patient occurred monthly for 6 months. At each visit, we collected four images of the infant’s ears, and the child’s weight. We analyze ear area versus age and change in ear area versus age. We conduct pair-wise comparisons for all age intervals. Results From 227 enrolled infants we acquired age-specific datasets for 6 days through 9 months. Maximal ear growth occurred between 6 days and 14 weeks. Growth was significant until 6 months of age, after which further growth appeared minimal. Examining look-back performance to the 6-month visit, baseline pair-wise comparisons yielded identification rates that ranged 46.9–75%. Concatenating left and right ears per participant improved identification rates to 61.5–100%. Concatenating images captured on adjacent visits further improved identification rates to 90.3–100%. Lastly, combining these two approaches improved identification to 100%. All matching strategies showed the weakest matching rates during periods of maximal growth (i.e., <6 months). Conclusion By quantifying the effect that ear growth has on performance of the SEARCH platform, we show that ear identification is a feasible solution for patient identification in an infant population 6 months and above.

156. Correlation Between WHO (World Health Organization) Case Definition of Severe Pneumonia and Lung POCUS (Point of Care Ultrasound) vs Chest X-ray (CXR) Findings to Diagnose Pediatric Community-Acquired Pneumonia (CAP) in Limited Resource Settings

Background

Childhood pneumonia is one of the leading causes of death in low-income countries. The diagnosis of pediatric pneumonia is a critical epidemiological duty for treatment effectiveness and vaccine surveillance. Previous studies have demonstrated an important lack in correlation between CXR findings and the clinical WHO case definition of severe pneumonia. Lung Point of Care Ultrasound (POCUS) has demonstrated in multiple studies to be more sensitive and specific for diagnosing pneumonia in the pediatric population. With no exposure to radiation, extensive availability in limited-resource settings, and easy interpretation, this modality can be a breakpoint in making a more accurate correlation between pneumonia clinical findings and diagnostic imaging.

Methods

50 children from 1-59 months meeting the WHO case definition of severe pneumonia were enrolled at the Emergency Department at University Teaching Hospital (UTH) in Lusaka, Zambia. Children underwent lung POCUS and CXR. Correlation between symptoms and all abnormalities (consolidation, effusion, and interstitial patterns) seen in both imaging modalities were analyzed by calculating the proportion of children with abnormalities on CXR and ultrasound. Each participant was assigned a score based on findings. 0 = normal, 1 = consolidation only, 2 = Consolidation and non-consolidation (interstitial and/or effusion) and 3 = non-consolidation (interstitial and/or effusion) only.

Results

44 (90%) of children had abnormalities on CXR and 46 (94%) on POCUS. Five children (10%) had normal findings on CXR vs 3 (6%) on Lung POCUS. 4 (8%) had consolidation only on CXR vs 0 (0%) on POCUS. 19 (39%) had consolidation and non-consolidation (interstitial and/or effusion) on CXR vs. 20 (41%) on POCUS. 21 (43%) had non-consolidation (interstitial and/or effusion) only on CXR vs. 26 (53%) on POCUS.

Figure 1. Scores Asigned Based on Imaging Findings for CXR and Lung POCUS

Figure 2. Chest X Ray Anterior Posterior (AP) view showing Bilareral Interstitial Pattern

Figure 3. Lung POCUS (Point of Care Ultrasound) findings of bilateral Consolidation and non-consolidation pattern and bilateral interstitial pattern (only finding on CXR)

Conclusion

More children with clinical pneumonia had normal findings on CXR than on POCUS. POCUS was a better imaging technique to show consolidation and non-consolidation patterns than CXR. The higher proportion of children diagnosed with consolidation and non-consolidation patterns on POCUS suggest that CXR might not be the ideal gold standard to diagnose pneumonia in children.

Disclosures

All Authors: No reported disclosures

732. Sensitivity and Specificity of Point of Care Lung Ultrasound vs. Chest X-Ray for the Diagnosis of Pediatric Pneumonia in Limited resource settings: The Zambia Experience

Background

Pediatric pneumonia is the leading cause of child mortality in low-income countries. Pneumonia diagnosis is a challenge. Chest x-ray (CXR) is considered the gold standard, but it exposes children to ionizing radiation, and access to CXR is limited to hospital settings. Lung Point of Care Ultrasound (POCUS) is a portable and non-radiating alternative to CXR.

Methods

We enrolled 200 children aged 1-59 months from the University Teaching Hospital (UTH) Emergency Department (ED) in Lusaka, Zambia who met the WHO (World Health Organization) case definition for severe pneumonia. From each child, we collected demographic and clinical data, a CXR, and a set of ultrasound images using a Butterfly ultrasound probe. Images were independently interpreted by two radiologists blinded to the results of the other imaging modality. Using CXR as the gold standard, we determined the sensitivity and specificity, positive and negative predictive values, and likelihood ratios for pneumonia using lung POCUS.

Results

This preliminary analysis included 50 children seen between May-October 2020. Median age (9 months) (Range 4-15). 58% were male, (29/50). Median temperature was 37.3⁰C (range 36.5-38.0); median respiratory and pulse rates were 41 breaths/min (range 31-50) and 139 beats/min (range 124-160) respectively; median SpO₂ on RA was 91% (range 89-95). 50% of cases had difficulty breathing (82%, 41/50); chest retractions (70%, 35/50) and grunting (62%, 31/50). Ultrasound images for 49/50 (98%) cases and CXRs for 50/50 (100%) of cases we analyzed. Sensitivity of lung POCUS in the detection of CAP was 61% (95% Cl: 0.52-0.84). The specificity was 77% (95% Cl: 0.56-0.91). Positive predictive value (PPV) 70% (95% CI: 0.62-0.94) and negative predictive value (NPV) 69% (95% CI: 0.56-0.79).

Conclusion

Preliminary findings of this study demonstrated the lower diagnostic accuracy of lung POCUS versus CXR in the detection of pneumonia in children 1- 59 months. The high specificity of the test will aid in ruling out severe pneumonia in children. Due to its availability, ease of interpretation, and absence of radiation exposure, lung POCUS should still be considered as an important initial imaging tool for the diagnosis of CAP in children in limited-resource settings.

Disclosures

All Authors: No reported disclosures

Relative advantages and compatibility of a biometric patient identification tool in Zambia: a qualitative analysis

Background: The Scanning Ears for Child Health (SEARCH) system is a biometric patient identification tool which uses a pattern recognition algorithm to translate an image of the ear into a unique identifier. If integrated into an electronic medical records (EMR) system, it would provide a patient identification solution that replaces unreliable paper, under-five card (UFC), or number-based identifiers. This study aims to understand the relative advantage of the biometric system, the sociocultural and pragmatic compatibility, and the extent of UFC deterioration over time. Methods: Interviews on impressions of the novel biometric patient identification tool were conducted in urban and rural settings in Zambia. Focus group discussions included 59 participants and key informant interviews included 5 healthcare workers and 2 government officials. Transcripts were coded into thematic categories for analysis. We sought to understand 1) the perceived relative advantage of a biometric system over the traditional UFCs among Zambian mothers, 2) the perceived sociocultural compatibility of a biometric system in the healthcare setting, and 3) pragmatic compatibility of the proposed system. Results: We found that the current UFC system presents issues for continuity of care and quality of data management, therefore posing disadvantages relative to the proposed system. Sociocultural and pragmatic barriers to acceptance included the existing fear of Satanism and electrical power issues throughout Zambia. Mothers and healthcare workers expressed that adoption of the biometric system could be successful given efforts to sensitize the community. Conclusions: Switching to an EMR backed by biometric identification would fill a critical gap in Zambian healthcare information systems and has numerous perceived advantages in both urban and rural settings. We determine that strategies for implementation should be localized, context informed, and conducted by trusted community members with knowledge of best approaches to diffusing information and a deep understanding of the novel biometric system.

Project SEARCH (Scanning EARs for Child Health): validating an ear biometric tool for patient identification in Zambia

Patient identification in low- to middle-income countries is one of the most pressing public health challenges of our day. Given the ubiquity of mobile phones, their use for health-care coupled with a biometric identification method, present a unique opportunity to address this challenge. Our research proposes an Android-based solution of an ear biometric tool for reliable identification. Unlike many popular biometric approaches (e.g., fingerprints, irises, facial recognition), ears are noninvasive and easily accessible on individuals across a lifespan. Our ear biometric tool uses a combination of hardware and software to identify a person using an image of their ear. The hardware supports an image capturing process that reduces undesired variability. The software uses a pattern recognition algorithm to transform an image of the ear into a unique identifier. We created three cross-sectional datasets of ear images, each increasing in complexity, with the final dataset representing our target use-case population of Zambian infants (N=224, aged 6days-6months). Using these datasets, we conducted a series of validation experiments, which informed iterative improvements to the system. Results of the improved system, which yielded high recognition rates across the three datasets, demonstrate the feasibility of an Android ear biometric tool as a solution to the persisting patient identification challenge.

Covid-19 deaths in Africa: prospective systematic postmortem surveillance study

OBJECTIVE

To directly measure the fatal impact of coronavirus disease 2019 (covid-19) in an urban African population.

DESIGN

Prospective systematic postmortem surveillance study.

SETTING

Zambia's largest tertiary care referral hospital.

PARTICIPANTS

Deceased people of all ages at the University Teaching Hospital morgue in Lusaka, Zambia, enrolled within 48 hours of death.

MAIN OUTCOME MEASURE

Postmortem 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.

RESULTS

372 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%).

CONCLUSIONS

Contrary 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.

Detailed four-way comparative mapping and gene order analysis of the canine ctvm locus reveals evolutionary chromosome rearrangements

Canine tricuspid valve malformation (CTVM) maps to canine chromosome 9 (CFA9), in a region syntenic with gene-dense human chromosome 17q. To define synteny blocks, we analyzed 148 markers on CFA9 using radiation hybrid mapping and established a four-way comparative map for human, mouse, rat, and dog. We identified a large number of rearrangements, allowing us to reconstruct the evolutionary history of individual synteny blocks and large chromosomal segments. A most parsimonious rearrangement scenario for all four species reveals that human chromosome 17q differs from CFA9 and the syntenic rodent chromosomes through two macroreversals of 9.2 and 23 Mb. Compared to a recovered ancestral gene order, CFA9 has undergone 11 reversals of <3 Mb and 2 reversals of >3 Mb. Interspecies reuse of breakpoints for micro- and macrorearrangements was observed. Gene order and content of the ctvm interval are best extrapolated from murine data, showing that multispecies genome rearrangement scenarios contribute to identifying gene content in canine mapping studies.

Genetic variation and inferences about perceived taste intensity in mice and men

The study of genetic variation in taste produces parallels between mice and men. In mice, genetic variation across strains has been documented with psychophysical and anatomical measures as well as with recordings from whole nerves. In humans, the variation has been documented with psychophysical and anatomical measures. Whole-nerve recordings from animals and psychophysical ratings of perceived intensities from human subjects have a similar logical limitation: absolute comparisons across individuals require a standard stimulus that can be assumed equally intense to all. Comparisons across whole-nerve recordings are aided by single-fiber recordings. Comparisons across psychophysical ratings of perceived intensity have been aided by recent advances in methodology; these advances now reveal that the magnitude of genetic variation in human subjects is larger than previously suspected. In females, hormones further contribute to variation in taste. There is evidence that the ability to taste (particularly bitter) cycles with hormones in women of child-bearing age, rises to a maximum early in pregnancy and declines after menopause. Taste affects food preferences, which in turn affect dietary behavior and thus disease risks. Valid assessment of taste variation now permits measurement of the impact of taste variation on health. Advances in psychophysical methodology were essential to understanding genetic variation in taste. In turn, the association of perceived taste intensities with tongue anatomy now provides a new tool for psychophysics. The ability of a psychophysical scale to provide across-subject comparisons can be assessed through its ability to show the fungiform papillae density-taste association.

Differential effects of mucosal pH on human (Caco-2) intestinal epithelial cell motility, proliferation, and differentiation

Mucosal pH abnormalities are associated with anastomotic dehiscence, ischemia, and malignancy. We postulated that intraluminal pH influences intestinal epithelial motility, proliferation, and differentiation and studied extracellular pHo (7.0-8.5) effects on human (Caco-2) intestinal epithelial motility, proliferation, and differentiation. Mucosal healing was modeled by sheet migration and differentiation by alkaline phosphatase and dipeptidyl dipeptidase specific activity. In parallel differentiation and motility studies, we inhibited proliferation with mitomycin to dissociate indirect mitogenic effects. Intracellular pHi was quantitated using BCECF/AM at varying extracellular pHo and in migrating cells. Motility was maximal at pHo 7.6 and proliferation at 7.2. Each decreased with acidity and alkalinity. By contrast, brush border enzyme activity was lowest at pHo 7.0 and highest at pHo 8.5. pHi was highest at pHo 8.5. Migrating cell pHi was higher than static cell pHi. Thus, extracellular pHo deviations perturb Caco-2 pHi homeostasis and motility. Alkalinity promotes differentiation while acidity induces proliferation and limits differentiation.

Teicoplanin-resistant Staphylococcus aureus expresses a novel membrane protein and increases expression of penicillin-binding protein 2 complex

In the recent clinical trials of teicoplanin therapy of endocarditis caused by Staphylococcus aureus, at least one instance of the emergence of teicoplanin-resistant strains during therapy has been reported (G.W. Kaatz, S. M. Seo, N. J. Dorman, and S. A. Lerner, J. Infect. Dis 162:103-108, 1990). We have confirmed, using conventional electrophoresis of EcoRI-digested chromosomal DNA and pulsed-field gel electrophoresis of SmaI-digested chromosomal DNA, that the resistant strain (12873) (MIC, 16 micrograms/ml) is genetically very similar to the susceptible parent (12871) (MIC, 4 micrograms/ml). Kaatz et al. were able to select spontaneous teicoplanin-resistant mutants (10(-9)), suggesting that a single gene might be involved. We have shown that the mutation is highly stable during growth in the absence of teicoplanin. Using Tn551, we have selected insertion mutants of 12873 that become teicoplanin susceptible. We have examined a number of aspects of cell wall physiology in strains 12871 and 12873 and the teicoplanin-susceptible Tn551 mutants of 12873. 12873 was more susceptible to lysostaphin lysis than 12871 and the susceptible Tn551 derivatives of 12873. Autolysis in phosphate buffer (pH 7.5) and cell wall turnover rates were similar in 12871 and 12873. An analysis of membrane proteins revealed the expression of a ca. 35-kDa protein and increased expression of both polypeptides of penicillin-binding protein (PBP) 2 (PBP2) in 12873 relative to 12871 and the Tn551 mutants of 12873. This increased expression was not related to PBP2', since both strains were susceptible to oxacillin in 2% NaCl (MIC, < or = 0.25 microgram/ml) and cellular DNA from neither strain hybridized with a specific mec gene probe. Two independent Tn551 inserts have been mapped to a ca. 117-kb SmaI fragment of the chromosome. These data suggest the possibility that the mutation resulting in resistance to teicoplanin involves the regulation of expression of both polypeptides of PBP2 and a 35-kDa membrane protein.

Resistance to cefoperazone-sulbactam in Klebsiella pneumoniae: evidence for enhanced resistance resulting from the coexistence of two different resistance mechanisms

We investigated the in vitro activity and the in vivo efficacy of the beta-lactam-beta-lactamase inhibitor combination cefoperazone-sulbactam against an isogenic series of Klebsiella pneumoniae strains. Both cefoperazone and cefoperazone-sulbactam were active in vitro against a susceptible clinical strain, and the combination was highly effective in the treatment of rat intra-abdominal abscesses. Loss of expression of a 39-kDa outer membrane protein resulted in at least a fourfold increase in the MICs of cefoperazone and cefoperazone-sulbactam but did not appreciably affect the in vivo efficacy of either regimen. Introduction of plasmid RP4, which encodes the TEM-2 beta-lactamase, into the susceptible strain resulted in the loss of in vitro activity and in vivo efficacy for cefoperazone. The in vitro activity of cefoperazone-sulbactam against this strain was diminished, but the antibiotic combination remained highly active in vivo. Introduction of RP4 into the strain lacking the 39-kDa outer membrane protein resulted in a fourfold increase in the in vitro MIC of cefoperazone-sulbactam in comparison with the beta-lactamase-producing susceptible strain and resulted in a loss of in vivo efficacy against infections caused by this strain. These results suggest that the combination of different resistance mechanisms, neither of which alone results in substantially diminished cefoperazone-sulbactam efficacy in vivo, can cause in vivo resistance to the beta-lactam-beta-lactamase inhibitor combination in K. pneumoniae.

Vancomycin resistance in Enterococcus gallinarum

The vancomycin resistance expressed by several strains of Enterococcus gallinarum was studied. Resistance was expressed constitutively, as demonstrated by analysis of growth and inhibition of peptidoglycan synthesis. E. gallinarum strains were moderately resistant to vancomycin (MIC, 16 micrograms/ml) but were as susceptible as vancomycin-susceptible enterococci to the glycopeptides, teicoplanin, A35512B, A47934, A4103A, and A41030E and the glycopeptide actaplanins A1, B2, and C1. Vancomycin resistance in E. gallinarum was inhibited by beta-lactam antibiotics at concentrations that saturated penicillin-binding protein 6 (PBP 6), as demonstrated by binding competition experiments. Spontaneous mutants (frequency, 10(-8)) were two- to fourfold more resistant to beta-lactam inhibition of vancomycin resistance than the parent strain. PBP binding competition experiments suggested that PBP 6 in the mutants bound less cefotaxime, while binding of penicillin and cefoxitin was unaffected. Both a bioassay method and high-performance liquid chromatography showed that E. gallinarum membranes have enzymatic activity which modifies a model pentapeptide yielding a product that is thought to be a tetrapeptide. This activity could be a D,D-carboxypeptidase. In both the parent E. gallinarum strain and its derivatives that were resistant to the synergistic drug combination, the activity was inhibited by beta-lactams at concentrations which correlated with those that inhibit vancomycin resistance and those that saturate PBP 6. These results suggest the possibility that PBP 6 may be involved in the vancomycin resistance of E. gallinarum and that the putative D,D-carboxypeptidase activity seen in E. gallinarum membranes may be attributable to PBP 6.

Synergistic killing of vancomycin-resistant enterococci of classes A, B, and C by combinations of vancomycin, penicillin, and gentamicin

Using both high and low inocula for time-kill curves, we examined the antibiotic killing of clinical isolates of glycopeptide-resistant enterococci (Enterococcus faecium, E. faecalis, and E. gallinarum) belonging to phenotypic resistance classes A, B, and C. None were resistant to high levels (greater than 500 mg/liter) of gentamicin. Vancomycin-penicillin-gentamicin resulted in 2 or more logs of killing above that of the most effective two-antibiotic combination for all strains except two of three E. gallinarum (VanC) strains and a constitutive mutant of a VanB strain. This strategy may be useful clinically.