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Pearse, Oliver (2023) Transmission of Extended-Spectrum Beta-Lactamase Klebsiella pneumoniae on the Chatinkha Neonatal unit, Blantyre, Malawi, Thesis (Doctoral), Liverpool School of Tropical Medicine.
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O Pearse_thesis_corrections_aug23_clean_v2.pdf - Accepted Version Restricted to Repository staff only until 7 May 2024. Download (6MB) |
Abstract
Background
Klebsiella pneumoniae is a Gram-negative bacillus that has emerged as a leading cause of neonatal and childhood infection, particularly in low- and middle-income countries. This species is of concern because of its ability to acquire antimicrobial resistance (AMR) genes, such as Extended Spectrum Beta-Lactamases (ESBLs), which make it resistant to 3rd generation cephalosporins such as ceftriaxone. It is an extremely diverse organism, with dozens of different sequence types (STs) responsible for human disease, and there is evidence of within host diversity. It is commonly acquired nosocomially. Prevention of K. pneumoniae is key, especially amongst the most vulnerable patients (i.e. neonates), which in healthcare settings requires the establishment of infection prevention and control (IPC). IPC is a practical, evidence-based approach that aims to prevent patients and healthcare workers from being harmed by avoidable infections. IPC is difficult to establish and sustain once established as it depends on multiple complex factors as diverse as human behaviours and health system resources. As such, optimal IPC practice will vary between location, including the best way of targeting IPC resources against K. pneumoniae. To rationally determine the best usage of IPC, an understanding of how the pathogen is transmitted to patients is vital. However, there is a limited understanding of this, most notably in the low- and middle-income countries where it is most prevalent. This thesis aims to describe the most important transmission routes of ESBL K. pneumoniae to inpatient neonates on a Malawian neonatal unit, to inform IPC practice.
Methods
We recruited 94 neonate-mother pairs admitted to the Chatinkha neonatal unit, in Malawi, and collected stool samples from them, as well as hand swabs from mothers, swaddling cloth samples and cot swabs at regular intervals. We also swabbed the general ward environment and staff hands weekly. We isolated ESBL K.pneumoniae using chromogenic ESBL selective agar, and speciated putative isolates using multiplexed melt-curve polymerase chain reaction (PCR). We performed single pick whole genome sequencing (WGS) and plate sweep metagenomics on selected samples. These were analysed bioinformatically to type organisms by ST, determine SNP distances and reconstruct bacterial phylogeny, both utilising WGS and plate-sweep metagenomic data. The outputs of these analyses were used in statistical models to identify transmission.
Results
K. pneumoniae was the largest cause of neonatal sepsis and meningitis, accounting for 332/1314 (25.3%) of isolates. Most isolates were ESBL producers. Most neonates in the study (69/94 [73%]) were exposed to antibiotics. There was rapid stool colonisation of neonates on the ward with ESBL bacteria, especially K. pneumoniae. The median time to colonisation for all ESBLs was 3 days (95% CI 2-4) and for K. pneumoniae was 5 days (95% CI 4-6). ESBL bacteria including K. pneumoniae were also found in all environmental locations tested. A Bayesian state transition model highlighted female sex (HR 2.13 [95% credible interval (CrI) 0.93-5.15]), oxygen therapy (HR 2.09 [95% CrI 0.89-5.13]) and antibiotics (HR1.89 [95% CrI 0.71-5.05]) as being risk factors for stool colonisation. There were 71 different STs from 482 K. pneumoniae isolates, with ST15 being the most commonly isolated (61/482 [12.75%]), both in neonatal stool and the ward in general. Increasing ward contamination with a given ST preceded cases of colonisation and neonatal sepsis, as well as increasing afterwards, indicating a potential positive feedback loop associated with colonisation and infection. Utilising SNP distance and a temporal signal to infer specific potential transmission events, the largest number of transmission events to neonate’s stool was from the cots (31/85[37%]), the ward environment (26/85[31%]), other neonates (13/85[15%]) and maternal hands (7/85[8%]). A Bayesian source attribution model confirmed that the greatest contribution to neonatal stool colonisation was from the cots (0.46 [95% CrI 0.08-0.79]) and maternal hands (0.39 [95% CrI 0.09-0.74]), with the environment contributing proportionally less (0 [95% CrI 0 - 0.35]) when the overall number of isolates from different sources was considered. Maternal stool colonisation did not appear to significantly contribute to neonatal transmission. Directed network modelling confirmed the effect of cots, oxygen therapy and neonatal antibiotics on the transmission of ESBL K. pneumoniae. Limited-diversity metagenomics confirmed that single pick WGS underestimates the within-sample diversity of K. pneumoniae (median of 2 STs per sample, with a range of 1-19), particularly in environmental samples, and this method generated pseudo-assemblies with epidemiologically informative SNPs. ST15 was found in higher relative abundance in neonatal stool (0.35 [95% CI 0.11-0.59] higher relative abundance for ST15 compared to other STs) but not maternal stool (0.05 [-0.65-0.76]relative abundance of ST15 compared to other STs), indicating it may be better adapted at colonising neonates.
Conclusions
K. pneumoniae is an important cause of neonatal infection and colonisation that is primarily nosocomially transmitted in our setting, with no evidence to support vertical maternal transmission as being common. Transmission between neonate’s stool, their cots, the ward environment, and maternal hands is particularly important. The relationship between neonatal infection or colonisation with strains of K. pneumoniae and their presence in the environment indicate that a positive feedback loop of ward contamination can occur, with neonates acting as bacterial amplifiers, and the cots and maternal hands acting as vectors of transmission. Spread of neonatal stool around the ward may be implicated in this process. Outbreak associated STs such as ST15 may be better adapted to colonising neonates than other STs and as such, more likely to be amplified. Within-sample diversity of K. pneumoniae is present and has the potential to affect the conclusions of similar studies. Further work in our setting should look at ways of interrupting transmission by focussing on maternal hand hygiene and cot decontamination. It should also look at identifying “early warning” markers to highlight when the levels of bacterial contamination on a ward pass an un-safe threshold.
| Item Type: | Thesis (Doctoral) | ||||
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| Subjects: | WC Communicable Diseases > WC 20 Research (General) WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 260 Enterobacteriaceae and other enteric infections WS Pediatrics > By Age Groups > WS 420 Newborn infants. Neonatology |
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| Faculty: Department: | Clinical Sciences & International Health > Clinical Sciences Department | ||||
| Depositing User: | Lynn Roberts-Maloney | ||||
| Date Deposited: | 07 Feb 2024 12:17 | ||||
| Last Modified: | 07 Feb 2024 12:17 | ||||
| URI: | https://archive.lstmed.ac.uk/id/eprint/23987 |
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