Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana.

Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp., urging the need for the magnitude of Campylobacter-associated diarrhoea to be established. In this survey, we have characterised the genomic diversity of Campylobacter spp. circulating in Botswana isolated from cases of diarrhoeal disease in humans (n = 20) and from those that colonised commercial broiler (n = 35) and free-range (n = 35) chickens. Phylogeny showed that the Campylobacter spp. isolated from the different poultry and human sources were highly related, suggesting that zoonotic transmission has likely occurred. We found that for Campylobacter spp. isolated from humans, broilers and free-range chickens, 52% was positive for tetO, 47% for gyrA-T86I, 72% for blaOXA-61, with 27% carrying all three resistance determinants. No 23S mutations conferring macrolide resistance were detected in this survey. In summary, our study provides insight into Campylobacter spp. in poultry reservoirs and in diarrhoeal patients, and the relevance for treatment regimens in Botswana

Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana.

Campylobacter spp. are a leading cause of bacterial enteritis worldwide, including countries in Africa, and have been identified by the World Health Organisation (WHO) as one of the high priority antimicrobial resistant pathogens. However, at present there is little knowledge on the prevalence, molecular epidemiology or antimicrobial susceptibility of Campylobacter spp. isolates in Botswana, both in patients and in the zoonotic context. Some data indicate that ~14% of diarrhoeal disease cases in a paediatric setting can be ascribed to Campylobacter spp., urging the need for the magnitude of Campylobacter-associated diarrhoea to be established. In this survey, we have characterised the genomic diversity of Campylobacter spp. circulating in Botswana isolated from cases of diarrhoeal disease in humans (n = 20) and from those that colonised commercial broiler (n = 35) and free-range (n = 35) chickens. Phylogeny showed that the Campylobacter spp. isolated from the different poultry and human sources were highly related, suggesting that zoonotic transmission has likely occurred. We found that for Campylobacter spp. isolated from humans, broilers and free-range chickens, 52% was positive for tetO, 47% for gyrA-T86I, 72% for blaOXA-61, with 27% carrying all three resistance determinants. No 23S mutations conferring macrolide resistance were detected in this survey. In summary, our study provides insight into Campylobacter spp. in poultry reservoirs and in diarrhoeal patients, and the relevance for treatment regimens in Botswana

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

Introduction 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. Methods 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 & templates (flat surfaces); 2) sterile syringe & tubing (water aspiration); and 3) structured swabbing techniques (hands & 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. Results 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 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. Conclusions 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, & 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.Medicine, Faculty ofNon UBCPathology and Laboratory Medicine, Department ofReviewedFacultyOthe

MLST of <i>C</i>. <i>coli</i> isolates from this study and other African <i>C</i>. <i>coli</i> isolates.

<p>Minimum spanning tree generated from <i>C</i>. <i>coli</i> allelic profiles visualised in GrapeTree [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194481#pone.0194481.ref025" target="_blank">25</a>], which included African <i>C</i>. <i>coli</i> isolates that were available in the PubMLST database [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194481#pone.0194481.ref024" target="_blank">24</a>] (accessed in January 2017). Isolates are colour-coded according to country and labelled with STs. The number of isolates per node (ST) are indicated through pie-charts. The number of nucleotide differences between STs is depicted at the branches. If STs differ by more than 2 nucleotides, branches are truncated (dashed lines). More details can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194481#pone.0194481.s001" target="_blank">S1 Table</a> and in the text.</p

Phylogeny and AMR profile of <i>C</i>. <i>coli</i> isolates from this study.

<p>Core genome maximum likelihood phylogeny of <i>C</i>. <i>coli</i> isolates visualised in the iTol [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194481#pone.0194481.ref023" target="_blank">23</a>]; the tree was rooted with isolate B15 as an outgroup. Clustering of isolates was found to be in accordance between core genome and SNP-based phylogenies (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194481#pone.0194481.s003" target="_blank">S2 Fig</a>). Isolates belonging to the same ST clustered together. Shown for each isolate are: isolate identifier, the geographic location os isolation, presence of AMR determinants and ST.</p

Phylogeny and AMR profile of <i>C</i>. <i>jejuni</i> isolates from this study.

<p>Core genome maximum likelihood phylogeny of <i>C</i>. <i>jejuni</i> isolates visualised in the interactive Tree of life tool (iTol) [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194481#pone.0194481.ref023" target="_blank">23</a>]. The tree was rooted on isolate 2445 to facilitate comparison with the SNP-based phylogeny shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194481#pone.0194481.s002" target="_blank">S1 Fig</a>. Clustering of isolates was found to be in accordance between core genome and SNP-based phylogenies (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0194481#pone.0194481.s002" target="_blank">S1 Fig</a>). Clustering of isolates belonging to the same ST was consistent. Shown for each isolate are: isolate identifier, the geographic location of isolation, presence of AMR determinants and ST.</p