Finola Catherine Leonard

Background: Antimicrobial resistance (AMR) poses a significant threat to global health and economic development. In Malawi, the economic costs associated with the treatment of AMR infections remain largely unknown which may hinder resource allocation and policy prioritization. Method: The study used a cross-sectional design and was conducted between September 2023 and January 2025 at three different hospital settings. Data were collected from inpatients with laboratory-confirmed urinary tract infection (UTI) or blood stream infection (BSI). Additional follow-up data were collected from patients for four weeks post discharge. We analyzed patient level data first using descriptive statistics and employed an instrumental variable 2-stage least squares regression to estimate drivers of AMR treatments costs. Results: A total of 610 patients participated in the study. Of these, 45% had AMR-associated resistant infections. Overall, E. coli (43%) followed by P. aeruginosa (22%), K. pneumoniae (14%), and S. aureus (10%) were the most common pathogens. UTI was marginally more common (51%) compared to BSI (49%). BSI had a higher average cost than UTI for patients with both susceptible and resistant infections. On average, a patient spent MK283,815.10 (US$163.71) ranging from zero to MK13,500,000 (US$7786.90). Patients with resistant infections incurred, on average, MK161,785 (US$93.32) more than patients with susceptible infections, largely driven by prolonged hospitalization among other factors. Overall, the direct medical observed costs averaged MK37,165.29 (US$21.44) while direct non-medical observed costs averaged MK61,908.71 (US$35.71). Productivity losses for the patient and guardian(s) were a major observed cost averaging MK160,322.80 (US$92.49). The regression results further showed that having a bank account as a proxy of wealth, non-farm business, longer travel duration, BSI, and K. pneumoniae as the causative pathogens were significantly associated with increased cost burden among the patients. Conclusions: AMR-associated infections impose substantial economic burden on patients and households. Further strengthening of AMR surveillance and stewardship are needed as critical elements of Malawi’s National Action Plan. However, measures should also be taken to mitigate the economic consequences related to AMR, especially for patients who bear the brunt of these costs for lack of financial protection in Malawi’s health system.

Over the past 20 years, the Integrated Constructed Wetland (ICW) concept has been applied in Ireland for wastewater treatment, offering a nature-based solution for reducing pollutants and antimicrobial resistance genes (ARGs) in effluents and receiving environments. However, wastewater microbial communities remain inadequately characterized and their dynamics across treatment largely unexplored. Here, we present a culture-independent investigation of four Irish ICWs, aiming to advance our understanding of microbial dynamics in wastewater treatment. Shotgun metagenomic sequencing was conducted on influent and effluent samples collected in biological triplicates from four ICWs treating agricultural, companion animal, industrial, and municipal wastewater, alongside eight positive and ten negative controls for filtering and sequencing. End-to-end metagenomic analysis was performed with SqueezeMeta. Taxonomic placement of high-quality metagenome-assembled-genomes (HQ-MAGs) was confirmed with GTDB-Tk. Decontamination and statistical analyses were conducted in R. Coassembled contigs were screened for ARGs, virulence- and plasmid-associated sequences. Results revealed statistically significant shifts in taxonomic and functional profiles across treatment. Effluent populations exhibited generally higher richness than corresponding influents, yet were more similar to one another across locations. Multi-log-scale increases were observed in the relative abundance of environmental genera (Legionella, Methylotenera, Thiothrix), alongside reductions in common faecal/human indicators (Bacteroides, Lactococcus, Prevotella), and up to 80% ARGs removal. Collectively, our findings provide insights into ICW efficacy, showing that they can drive marked shifts in wastewater microbiome and ARG reduction. Our culture-independent approach retrieved 34 HQ-MAGs, including 19 potentially novel taxa, uncovering previously uncharacterized microbial diversity that is potentially unique to the Irish environment and warrants further investigation.

Background: Antimicrobial resistance (AMR) poses a significant threat to global health and economic development. In Malawi, the economic costs associated with AMR remain largely unknown which may hinder resource allocation and policy prioritization. Method: The study used instrumental variable 2-stage least squares regression to analyze patient level cost data at tertiary and secondary level facilities primarily collected from 610 patients with urinary tract infection (UTI) or blood stream infection (BSI) using a questionnaire. Results: Findings indicate that E. coli (43%) followed by K. pneumoniae (14%), and S. aureus (10%) were common pathogens overall. UTI was common (51%) compared to BSI (49%) yet BSI had a higher average cost than UTI for both susceptible and resistant patient categories. In terms of costs, a patient spent MK283,815.10 (US$163.71) on average as a result of AMR infection. The total cost reached as high as MK13,500,000 (US$7,786.90). Patients with a resistant infection incurred, on average MK161,785 (US$93.32) more than patients whose infection was susceptible, with the additional costs being driven by prolonged hospitalization among other factors. The direct medical costs averaged MK37,165.29 (US$21.44) while direct non-medical costs averaged MK61,908.71 (US$35.71). Productivity losses for the patient and guardian(s) were a major cost averaging MK160,322.80 (US$92.49). The regression results further showed that having a bank account as a proxy of wealth, non-farm business, longer travel duration, BSI, and K. pneumoniae as causing pathogens were significantly associated with increased cost burden among the patients. Conclusions: AMR imposes substantial economic burden on Malawi's health system, with most costs falling on patients. Further strengthening of AMR surveillance and stewardship are needed as critical elements of Malawi’s National Action Plan. However, measures should also be taken to mitigate the economic consequences related to AMR, especially for patients who bear the brunt of these costs for lack of financial protection in Malawi’s health system.

Bovine intramammary infection (IMI) has a negative impact on the dairy industry through economic loss, increased antibiotic use, and reduced animal welfare. Major infectious agents include Staphylococcus aureus, non-aureus staphylococci and mammaliicocci (NASM), streptococci, and coliforms such as Escherichia coli, with the pathogen profile influenced by geography and production system. Strain variability, particularly for S. aureus, also affects the severity and epidemiology of IMI. To investigate the genetic variability of bovine S. aureus and determine if herd-level and individual cow milk quality parameters are associated with specific IMI pathogens or S. aureus genotypes, 20 Irish dairy herds were studied. These herds were classified as problem herds, i.e., high within-herd prevalence of sub-clinical mastitis based on cow level somatic cell counts (SCC) (n = 10), or control, i.e., low within-herd prevalence of sub-clinical mastitis (n = 10). Milk samples were collected from putatively infected primiparous and multiparous cows and subjected to microbiological, milk composition and milk processing analyses. The major pathogens isolated were NASM (37%), streptococci (17%) and S. aureus (13%) with no microorganism recovered from 29% of samples. The majority of S. aureus isolates belonged to Clonal Complex (CC) 97 or CC151 and S. aureus lineage was significantly associated with farm status; CC97 was 10 times more likely to be isolated from a problem than a control herd whereas CC151 was 5.6 times more likely to be recovered from a control than a problem herd. SCC was dependent on the nature of the infecting agent. For all bacterial species, positive samples had significantly higher SCC than samples that were bacteriologically negative, with milk containing S. aureus having significantly higher SCC than all other groups. Infectious agent was also associated with total solids, lactose percentage and rennet coagulation time, although there were no differences between S. aureus lineages in SCC, milk composition or processing parameters. Antimicrobial resistance was rare among the S. aureus isolates, although CC97 and CC8 isolates were resistant to penicillin and ampicillin. Comparative genomic analysis of the S. aureus isolates identified lineage-associated virulence genes. Pan-genome analysis identified a small number of CC97 and CC151 unique genes although no functional enrichment of the unique genes was identified. A number of the lineage-unique genes were associated with mobile genetic elements.

An 11-year-old male neutered domestic shorthair cat underwent investigations for right mandibular and prescapular lymph node enlargement and weight loss. Cytology of the mandibular and prescapular lymph nodes revealed marked pyogranulomatous inflammation and mild neutrophilic, non-septic inflammation, respectively. Excisional biopsy of both lymph nodes was performed. Histopathology of the mandibular lymph node revealed severe pyogranulomatous inflammation, with prominent Splendore–Hoeppli phenomenon. Histopathology of the prescapular lymph node was consistent with reactive lymphoid hyperplasia. A Neisseria species was cultured from tissue samples obtained from both lymph nodes, with sensitivity testing confirming susceptibility to amoxicillin-clavulanate. After a 4-week course of amoxicillin-clavulanate (20 mg kg−1 PO q12h), clinical signs resolved. The cat was clinically well with no evidence of recurrence of infection 2.5 years after presentation.

Antimicrobial resistance (AMR) in Escherichia coli of animal origin presents a threat to human health. Although animals are not the primary source of human infections, humans may be exposed to AMR E. coli of animal origin and their AMR genes through the food chain, direct contact with animals, and via the environment. For this reason, AMR in E. coli from food producing animals is included in most national and international AMR monitoring programmes and is the subject of a large body of research. As pig farming is one of the largest livestock sectors and the one with the highest antimicrobial use, there is considerable interest in the epidemiology of AMR in E. coli of porcine origin. This literature review presents an overview and appraisal of current knowledge of AMR in commensal E. coli of the porcine gastrointestinal tract with a focus on its evolution during the pig lifecycle and the relationship with antimicrobial use. It also presents an overview of the epidemiology of resistance to extended spectrum cephalosporins, fluoroquinolones, and colistin in pig production. The review highlights the widespread nature of AMR in the porcine commensal E. coli population, especially to the most-used classes in pig farming and discusses the complex interplay between age and antimicrobial use during the pig lifecycle.

Staphylococci figure prominently among those bacteria demonstrating antimicrobial resistance (AMR) and are thus responsible for significant problems concerning the treatment of the animals and humans that they infect

Background: The main purpose of this study was to investigate the cleanliness and microbial burden of a veterinary hospital to establish the extent of cross-contamination with faecal bacteria as an aid to reducing nosocomial infections. Enterococci and Escherichia coli were used as faecal indicator organisms as they can survive on inanimate surfaces for months and pose a threat to animal health. The study consisted of several elements: (i) a cross-sectional study to identify sites currently contaminated with faecal organisms that could be usefully included in a longitudinal study, (ii) a 3-week longitudinal study to identify sites from which faecal bacteria were repeatedly recovered, (iii) once-off monitoring of hand hygiene, (iv) a review of all hospitalised cases with confirmed E. coli or enterococcal infection during the 8-week study period to investigate possible hospital-acquired (HAI) infection and relationship with environmental contamination. Environmental surface and hand hygiene were assessed using 3M™ Clean-Trace™ ATP test, 3M™ Petrifilm™ plates and bacteriological culture of Enterococcus species and E. coli. Cross contamination was assessed using results of antimicrobial susceptibility testing. Results: In the cross-sectional study, 26 of 113 (24.5%) of sites sampled exceeded the accepted microbial threshold (2.5 CFU/cm²) and Enterococcus species were isolated from 31 (27.4%) and E. coli from 9 (7.9%) of 113 samples. Organic residue and microbial levels were high in the dog kennels even after cleaning and faecal organisms were also recovered from sites such as the dispensary, a student computer and staff common room. Four of 51 (7.8%) hand samples were contaminated with faecal bacteria. Nine sites were monitored on three occasions in the longitudinal study and a total of 23 Escherichia coli and 6 Enterococcus species were recovered. Seven of the nine sites were positive for faecal organisms on more than one occasion. There was no change in cleanliness or microbial burden over 3 weeks. Twenty-one of the 73 isolates (28.8%) recovered during all parts of the study were multi-drug resistant. Enterococci and E. coli isolates with similar resistance patterns were recovered from the environment in the large and small animal hospitals and from a small number of patients during the same timeframe, suggesting possible hospital acquired infections. Conclusions: Results suggested that movement between the small and large animal hospital areas may have been responsible for cross-contamination and possible hospital-acquired infections. The data show that cross-sectional and longitudinal monitoring of faecal contamination across all hospital areas can play an important role in informing review of infection control protocols in veterinary hospital settings. Changes in practices in the hospital based on results generated are outlined.

The threat to public health posed by antimicrobial resistance in livestock production means that the pig sector is a particular focus for efforts to reduce antimicrobial use (AMU). This study sought to investigate the risk factors for AMU in Irish pig production. Antimicrobial use data were collected from 52 farrow-to-finish farms. The risk factors investigated were farm characteristics and performance, biosecurity practices, prevalence of pluck lesions at slaughter and serological status for four common respiratory pathogens and vaccination and prophylactic AMU practices. Linear regression models were used for quantitative AMU analysis and risk factors for specific AMU practices were investigated using logistic regression. Farms that milled their own feed had lower total AMU (p < 0.001), whereas higher finisher mortality (p = 0.043) and vaccinating for swine influenza (p < 0.001) increased AMU. Farms with higher prevalence of pericarditis (p = 0.037) and lung abscesses (p = 0.046) used more group treatments. Farms with higher prevalence of liver milk spot lesions (p = 0.018) and farms practising prophylactic AMU in piglets (p = 0.03) had higher numbers of individual treatments. Farms practising prophylactic AMU in piglets (p = 0.002) or sows (p = 0.062) had higher use of cephalosporins and fluoroquinolones. This study identified prophylactic use and respiratory disease as the main drivers for AMU in Irish pig production. These findings highlight areas of farm management where interventions may aid in reducing AMU on Irish pig farms.