Carbapenem-resistant <i>Acinetobacter baumannii</i> at a hospital in Botswana: detecting a protracted outbreak using whole genome sequencing
Notice bibliographique
Résumé
ABSTRACT Carbapenem-resistant Acinetobacter baumannii (CRAb) has emerged as a major and often fatal cause of bloodstream infections among hospitalized patients in low- and middle-income countries (LMICs). CRAb outbreaks are hypothesized to arise from reservoirs in the hospital environment, but outbreak investigations in LMICs are often limited in scope due to lack of access to whole genome sequencing (WGS). We performed WGS on 43 stored isolates (blood cultures [ n = 23] and environmental swabs [ n = 20]) presumptively identified as A. baumannii collected during 2021–2022 from a 530-bed referral hospital in Gaborone, Botswana, where CRAb infection incidence was rising. Taxonomic assignment, multilocus sequence typing, antimicrobial resistance gene identification, K and O locus typing, and phylogenetic analyses were performed using publicly accessible analysis pipelines. All 23 blood and 25% (5/20) of environmental isolates were confirmed as A. baumannii, 79% ( n = 22) of which were sequence type 1 (ST1). All ST1 isolates harbored genes encoding carbapenemases ( bla NDM-1 , bla OXA-23 ). Phylogenetic analysis demonstrated that nearly identical ST1 isolates spanned wide ranges in time (>1 year), suggesting ongoing transmission from environmental sources. One highly similar clade (average difference of 2.3 single nucleotide polymorphisms) contained all eight neonatal blood isolates and three environmental isolates from the neonatal unit. Environmental isolates included a sample from a sink drain, which is likely a major reservoir in this setting and highlights the need for targeted environmental remediation. Using a phylogenetically informed approach, we also identified diagnostic genes that distinguish this outbreak clone. These markers hold the potential to provide a low-cost method for tracking future CRAb isolates related to this outbreak. IMPORTANCE Carbapenem-resistant Acinetobacter baumannii is an increasingly significant cause of hospital-acquired bloodstream infections, particularly in low- and middle-income countries where limited resources often prevent the use of advanced outbreak investigation methods. This study leveraged whole genome sequencing to uncover transmission patterns of these antibiotic-resistant infections which were occurring more frequently in a referral hospital in Botswana. By linking clinical and environmental samples collected over an 18-month period, we identified a cluster of infections genetically linked to samples collected from the environment, including a sample taken from a sink drain in the neonatal unit. Furthermore, the study identified key genes specific to outbreak strains that could be used as diagnostic markers to track future outbreaks, even in the absence of genomic sequencing. These findings demonstrate how combining genomic sequencing with targeted gene identification can guide infection prevention and control efforts, helping to curb the spread of antibiotic resistance in resource-limited settings.
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Comment cette classification a été obtenuedéplier
Prédiction distillée sur la base complète
Imitation des enseignantsNi prévalence calibrée, ni vérité terrain. Validation humaine à venir. Apprise à partir de 10 348 étiquettes directes de Codex et de 10 348 étiquettes directes de Gemma. Le mode candidate est l'union des têtes enseignantes seuillées; le consensus est leur intersection. Ces sorties portent le statut machine_predicted_unvalidated et ne sont ni des étiquettes humaines ni des étiquettes directes de modèles de pointe.
Scores Codex et Gemma par catégorie
| Catégorie | Codex | Gemma |
|---|---|---|
| Métarecherche | 0,000 | 0,000 |
| Méta-épidémiologie (sens strict) | 0,000 | 0,000 |
| Méta-épidémiologie (sens large) | 0,000 | 0,000 |
| Bibliométrie | 0,000 | 0,000 |
| Études des sciences et des technologies | 0,000 | 0,000 |
| Communication savante | 0,000 | 0,000 |
| Science ouverte | 0,000 | 0,000 |
| Intégrité de la recherche | 0,000 | 0,000 |
| Charge utile insuffisante (le modèle a refusé de juger) | 0,000 | 0,000 |
Scores machine (provisoires)
Les deux têtes enseignantes du modèle étudiant, lues sur ce travail. Un score ordonne la base pour la relecture; il n'affirme jamais une catégorie, et le statut de validation accompagne chaque rangée tel quel.
Scores de référence d'un modèle non mature (critères de maturité non atteints, 7 itérations). Un score ordonne; il n'affirme jamais une catégorie.
score_only:v0-immature-baseline · tel quel depuis la passe de notation : score_only signifie que le nombre peut ordonner les travaux, et qu'aucune étiquette de catégorie n'en découleClassification
machine, non validéePrédiction automatique; un appel candidat d’une seule tête enseignante, pas un consensus.
Le détail, modèle par modèle et score par score, se trouve en fin de page sous « Comment cette classification a été obtenue ».