First name
Tonya
Last name
Arscott-Mills

Title

Evaluation of Anatomically Designed Flocked Rectal Swabs for Use with the Biofire FilmArray™ Gastrointestinal Panel for Detection of Enteric Pathogens in Children Admitted to Hospital with Severe Gastroenteritis.

Year of Publication

2019

Date Published

2019 Sep 11

ISSN Number

1098-660X

Abstract

Diagnosing diarrheal disease is difficult in part due to challenges in obtaining and transporting a bulk stool specimen, particularly in resource-limited settings. We compared the performance of flocked rectal swabs to that of traditional bulk stool samples for enteric pathogen detection using the BioFire™ FilmArray Gastrointestinal panel in children admitted to 4 hospitals in Botswana with community onset severe gastroenteritis. Of the 117-matched flocked rectal swab/stool pairs, we found no significant difference in pathogen detection rates between the flocked rectal swab samples and traditional bulk stool sampling methods for any bacterial (168 versus 167, respectively), viral (94 versus 92, respectively), or protozoan (18 versus 18, respectively) targets. The combination of flocked rectal swab samples with FilmArray testing allows for the rapid diagnosis of infectious gastroenteritis, facilitating a test and treat approach for infections that are life-threatening in many resource-limited settings. Culture recovery rates for bacterial pathogens utilizing this approach need to be assessed.

DOI

10.1128/JCM.00962-19

Alternate Title

J. Clin. Microbiol.

PMID

31511336

Title

'That's when I struggle' … Exploring challenges faced by care givers of children with tuberculosis in Botswana.

Year of Publication

2016

Number of Pages

1314-1319

Date Published

2016 Oct

ISSN Number

1815-7920

Abstract

SETTING: Government-funded public health clinics in and around Gaborone, Botswana.

OBJECTIVE: To explore the challenges faced by care givers of children on treatment for tuberculosis (TB) to inform a more child-friendly approach to Botswana's National TB Programme (NTP) strategy.

DESIGN: Qualitative study using 28 in-depth interviews with care givers of children receiving anti-tuberculosis treatment.

RESULTS: Care givers identified five main challenges: long delays in their child's diagnosis, difficulty attending clinic for daily treatment, difficulty administering TB medications, stock-outs of TB medications leading to treatment interruptions, and inadequate TB education. Care givers prioritized these same five areas to improve the overall management of their child's TB.

CONCLUSION: Our findings suggest that despite accessing care through an NTP that adheres to World Health Organization guidelines, care givers for children on treatment in Botswana continue to encounter significant challenges. While each of these represents a potential threat to successful treatment, they can be addressed with relatively small systematic and programmatic adjustments. These results will inform the next version of the Botswana NTP guidelines towards a more child- and care giver-centered approach.

DOI

10.5588/ijtld.15.0989

Alternate Title

Int. J. Tuberc. Lung Dis.

PMID

27725041

Title

Optimising the management of childhood acute diarrhoeal disease using a rapid test-and- treat strategy and/or Lactobacillus reuteri DSM 17938: a multicentre, randomised, controlled, factorial trial in Botswana.

Year of Publication

2022

Date Published

2022 Apr

ISSN Number

2059-7908

Abstract

<p><strong>INTRODUCTION: </strong>The study aim was to determine if rapid enteric diagnostics followed by the provision of targeted antibiotic therapy ('test-and-treat') and/or&nbsp;<em>Lactobacillus reuteri</em> DSM 17938 would improve outcomes in children hospitalised in Botswana with acute gastroenteritis.</p>

<p><strong>METHODS: </strong>This was a multicentre, randomised, factorial, controlled, trial. Children aged 2-60 months admitted for acute non-bloody diarrhoea to four hospitals in southern Botswana were eligible. Participants were assigned to treatment groups by web-based block randomisation. Test-and-treat results were not blinded, but participants and research staff were blinded to <em>L. reuteri</em>/placebo assignment; this was dosed as 1×10<sup>8</sup> cfu/mL by mouth daily and continued for 60 days. The primary outcome was 60-day age-standardised height (HAZ) adjusted for baseline HAZ. All analyses were by intention to treat. The trial was registered at Clinicaltrials.gov.</p>

<p><strong>RESULTS: </strong>Recruitment began on 12 June 2016 and continued until 24 October 2018. There were 66 participants randomised to the test-and-treat plus <em>L. reuteri&nbsp;</em>group, 68 randomised to the test-and-treat plus placebo group, 69 to the standard care plus <em>L. reuteri&nbsp;</em>group and 69 to the standard care plus placebo group. There was no demonstrable impact of the test-and-treat intervention (mean increase of 0.01 SD, 95% CI -0.14 to 0.16 SD) or the&nbsp;<em>L. reuteri</em> intervention (mean decrease of 0.07 SD, 95% CI -0.22 to 0.08 SD) on adjusted HAZ at 60 days.</p>

<p><strong>CONCLUSIONS: </strong>In children hospitalised for acute gastroenteritis in Botswana, neither a test-and-treat algorithm targeting enteropathogens, nor a 60-day course of <em>L. reuteri&nbsp;</em>DSM 17938, were found to markedly impact linear growth or other important outcomes. We cannot exclude the possibility that test-and-treat will improve the care of children with significant enteropathogens (such as <em>Shigella</em>) in their stool.</p>

<p><strong>TRIAL REGISTRATION NUMBER: </strong>NCT02803827.</p>

DOI

10.1136/bmjgh-2021-007826

Alternate Title

BMJ Glob Health

PMID

35418412

Title

Characterizing the bioburden of ESBL-producing organisms in a neonatal unit using chromogenic culture media: a feasible and efficient environmental sampling method.

Year of Publication

2022

Number of Pages

14

Date Published

2022 01 24

ISSN Number

2047-2994

Abstract

<p><strong>INTRODUCTION: </strong>Infections due to extended spectrum beta-lactamase producing organisms (ESBL) have emerged as the leading cause of sepsis among hospitalized neonates in Botswana and much of sub-Saharan Africa and south Asia. Yet, ESBL reservoirs and transmission dynamics within the neonatal intensive care unit (NICU) environment are not well-understood. This study aimed to assess the efficiency and feasibility of a chromogenic-culture-media-based environmental sampling approach to characterize the ESBL bioburden within a NICU.</p>

<p><strong>METHODS: </strong>A series of four point-prevalence surveys were conducted at a 36-bed NICU at a public tertiary referral hospital in Botswana from January-June 2021. Samples were collected on 4 occasions under semi-sterile technique using 1) flocked swabs &amp; templates (flat surfaces); 2) sterile syringe &amp; tubing (water aspiration); and 3) structured swabbing techniques (hands &amp; equipment). Swabs were transported in physiological saline-containing tubes, vortexed, and 10 µL was inoculated onto chromogenic-agar that was selective and differential for ESBL (CHROMagar™ ESBL, Paris, France), and streaking plates to isolate individual colonies. Bacterial colonies were quantified and phenotypically characterized using biochemical identification tests.</p>

<p><strong>RESULTS: </strong>In total, 567 samples were collected, 248 (44%) of which grew ESBL. Dense and consistent ESBL contamination was detected in and around sinks and certain high-touch surfaces, while transient contamination was demonstrated on medical equipment, caregivers/healthcare worker hands, insects, and feeding stations (including formula powder). Results were available within 24-72&nbsp;h of collection. To collect, plate, and analyse 50 samples, we estimated a total expenditure of $269.40 USD for materials and 13.5 cumulative work hours among all personnel.</p>

<p><strong>CONCLUSIONS: </strong>Using basic environmental sampling and laboratory techniques aided by chromogenic culture media, we identified ESBL reservoirs (sinks) and plausible transmission vehicles (medical equipment, infant formula, hands of caregivers/healthcare workers, &amp; insects) in this NICU environment. This strategy was a simple and cost-efficient method to assess ESBL bioburden and may be feasible for use in other settings to support ongoing infection control assessments and outbreak investigations.</p>

DOI

10.1186/s13756-021-01042-2

Alternate Title

Antimicrob Resist Infect Control

PMID

35074019

Title

Evolution of pneumococcal serotype epidemiology in Botswana following introduction of 13-valent pneumococcal conjugate vaccine.

Year of Publication

2022

Number of Pages

e0262225

Date Published

2022

ISSN Number

1932-6203

Abstract

<p>Pneumococcal conjugate vaccines reduce the burden of invasive pneumococcal disease, but the sustained effect of these vaccines can be diminished by an increase in disease caused by non-vaccine serotypes. To describe pneumococcal serotype epidemiology in Botswana following introduction of 13-valent pneumococcal conjugate vaccine (PCV-13) in July 2012, we performed molecular serotyping of 268 pneumococcal strains isolated from 221 children between 2012 and 2017. The median (interquartile range) age of the children included in this analysis was 6 (3,12) months. Fifty-nine percent of the children had received at least one dose of PCV-13 and 35% were fully vaccinated with PCV-13. While colonization by vaccine serotypes steadily declined following PCV-13 introduction, 25% of strains isolated more than 3 years after vaccine introduction were PCV-13 serotypes. We also observed an increase in colonization by non-vaccine serotypes 21 and 23B, which have been associated with invasive pneumococcal disease and antibiotic resistance in other settings.</p>

DOI

10.1371/journal.pone.0262225

Alternate Title

PLoS One

PMID

34986196

Title

Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy.

Year of Publication

2021

Date Published

2021 Sep 11

ISSN Number

1751-7370

Abstract

<p>Streptococcus pneumoniae (pneumococcus) is a leading cause of severe infections among children and adults. Interactions between commensal microbes in the upper respiratory tract and S. pneumoniae are poorly described. In this study, we sought to identify interspecies interactions that modify the risk of S. pneumoniae colonization during infancy and to describe development of the upper respiratory microbiome during infancy in a sub-Saharan African setting. We collected nasopharyngeal swabs monthly (0-6 months of age) or bimonthly (6-12 months of age) from 179 mother-infant dyads in Botswana. We used 16S ribosomal RNA gene sequencing to characterize the nasopharyngeal microbiome and identified S. pneumoniae colonization using a species-specific PCR assay. We detect S. pneumoniae colonization in 144 (80%) infants at a median age of 71 days and identify a strong negative association between the relative abundance of the bacterial genera Corynebacterium within the infant nasopharyngeal microbiome and the risk of S. pneumoniae colonization. Using in vitro cultivation experiments, we demonstrate growth inhibition of S. pneumoniae by secreted factors from strains of several Corynebacterium species isolated from these infants. Finally, we demonstrate that antibiotic exposures and the winter season are associated with a decline in the relative abundance of Corynebacterium within the nasopharyngeal microbiome, while breastfeeding is associated with an increase in the Corynebacterium relative abundance. Our findings provide novel insights into the interspecies interactions that contribute to colonization resistance to S. pneumoniae and suggest that the nasopharyngeal microbiome may be a previously unrecognized mechanism by which environmental factors influence the risk of pneumococcal infections during childhood. Moreover, this work lays the foundation for future studies seeking to use targeted manipulation of the nasopharyngeal microbiome to prevent infections caused by S. pneumoniae.</p>

DOI

10.1038/s41396-021-01108-4

Alternate Title

ISME J

PMID

34511605

Title

Effect of Haemophilus influenzae type b and 13-valent pneumococcal conjugate vaccines on childhood pneumonia hospitalizations and deaths in Botswana.

Year of Publication

2020

Date Published

2020 Jul 08

ISSN Number

1537-6591

Abstract

<p><strong>BACKGROUND: </strong>Globally, pneumonia is the leading cause of death among children. Few data exist regarding the effect of Haemophilus influenzae type b (Hib) vaccine and 13-valent pneumococcal conjugate vaccine (PCV-13) on the burden of childhood pneumonia in African settings.</p>

<p><strong>METHODS: </strong>We collected data on children 1 to 59 months of age at three hospitals in Botswana. Hib vaccine and PCV-13 were introduced in Botswana in November 2010 and July 2012, respectively. We compared pneumonia hospitalizations and deaths pre-vaccine (January 2009 to October 2010) to post-vaccine (January 2013 to December 2017) using seasonally-adjusted interrupted time-series analyses.</p>

<p><strong>FINDINGS: </strong>We identified 6943 pneumonia hospitalizations and 201 pneumonia deaths. In the pre-vaccine period, pneumonia hospitalizations and deaths increased by 24% (rate: 1.24; 95% CI: 0.94, 1.64) and 59% (rate: 1.59; 95% CI: 0.87, 2.90) per year, respectively. Vaccine introduction was associated with a 48% (95% CI: 29%, 62%) decrease in the number of pneumonia hospitalizations and a 50% (95% CI: 1%, 75%) decrease in the number of pneumonia deaths between the end of the pre-vaccine period (October 2010) and the beginning of the post-vaccine period (January 2013). During the post-vaccine period, pneumonia hospitalizations and deaths declined by 6% (rate 0.94; 95% CI: 0.89, 0.99) and 22% (rate: 0.78; 95% CI: 0.67, 0.92) per year, respectively.</p>

<p><strong>INTERPRETATION: </strong>Pneumonia hospitalizations and deaths among children declined sharply following introduction of Hib vaccine and PCV-13 in Botswana. This effect was sustained for more than five years after vaccine introduction, supporting the long-term effectiveness of these vaccines in preventing childhood pneumonia in Botswana.</p>

DOI

10.1093/cid/ciaa919

Alternate Title

Clin. Infect. Dis.

PMID

32634831

Title

Interpretation of pediatric chest radiographs by non-radiologist clinicians in Botswana using World Health Organization criteria for endpoint pneumonia.

Year of Publication

2020

Number of Pages

913-922

Date Published

2020 Jun

ISSN Number

1432-1998

Abstract

<p><strong>BACKGROUND: </strong>In low- and middle-income countries, chest radiographs are most frequently interpreted by non-radiologist clinicians.</p>

<p><strong>OBJECTIVE: </strong>We examined the reliability of chest radiograph interpretations performed by non-radiologist clinicians in Botswana and conducted an educational intervention aimed at improving chest radiograph interpretation accuracy among non-radiologist clinicians.</p>

<p><strong>MATERIALS AND METHODS: </strong>We recruited non-radiologist clinicians at a referral hospital in Gaborone, Botswana, to interpret de-identified chest radiographs for children with clinical pneumonia. We compared their interpretations with those of two board-certified pediatric radiologists in the United States. We evaluated associations between level of medical training and the accuracy of chest radiograph findings between groups, using logistic regression and kappa statistics. We then developed an in-person training intervention led by a pediatric radiologist. We asked participants to interpret 20 radiographs before and immediately after the intervention, and we compared their responses to those of the facilitating radiologist. For both objectives, our primary outcome was the identification of primary endpoint pneumonia, defined by the World Health Organization as presence of endpoint consolidation or endpoint effusion.</p>

<p><strong>RESULTS: </strong>Twenty-two clinicians interpreted chest radiographs in the primary objective; there were no significant associations between level of training and correct identification of endpoint pneumonia; concordance between respondents and radiologists was moderate (κ=0.43). After the training intervention, participants improved agreement with the facilitating radiologist for endpoint pneumonia from fair to moderate (κ=0.34 to κ=0.49).</p>

<p><strong>CONCLUSION: </strong>Non-radiologist clinicians in Botswana do not consistently identify key chest radiographic findings of pneumonia. A targeted training intervention might improve non-radiologist clinicians' ability to interpret chest radiographs.</p>

DOI

10.1007/s00247-020-04625-0

Alternate Title

Pediatr Radiol

PMID

32524176

Title

TB and TB-HIV care for adolescents and young adults.

Year of Publication

2020

Number of Pages

240-249

Date Published

2020 Feb 01

ISSN Number

1815-7920

Abstract

<p>Nine high-burden public tuberculosis (TB) clinics in Gaborone, Botswana. To evaluate the challenges encountered, healthcare worker (HCW) approaches, and supported interventions in TB and TB-HIV (human immunodeficiency virus) care for adolescents and young adults (AYA, aged 10-24 years). Semi-structured interviews with HCW in TB clinics, analyzed using thematic analysis. Sixteen HCWs were interviewed. AYA developmental needs included reliance on family support for care, increasing autonomy, attending school or work, building trust in HCWs, and intensive TB education and adherence support. Stigma strongly influenced care engagement, including clinic attendance and HIV testing. Health system barriers to optimal AYA TB care included limited staffing and resources to follow-up or support. HCWs utilized intensive education and counseling, and transitioned AYA to community-based directly observed therapy whenever feasible. HCWs supported implementation of youth-friendly services, such as AYA-friendly spaces or clinic days, training in AYA care, use of mobile applications, and peer support interventions, in addition to health system strengthening. HCWs utilize dedicated approaches for AYA with TB, but have limited time and resources for optimal care. They identified several strategies likely to improve care and better retain AYAs in TB treatment. Further work is needed to study interventions to improve AYA TB care and outcomes.</p>

DOI

10.5588/ijtld.19.0416

Alternate Title

Int. J. Tuberc. Lung Dis.

PMID

32127110

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