Mapping the flow of veterinary antibiotics in Kenya.

Introduction: To effectively regulate and reduce antibiotic use, in the livestock sector, a thorough understanding of the flow of veterinary antibiotics will help to identify key nodes in the chain for targeted interventions. The aim of this study was to understand the flow of antibiotics from import to end-user, and identify relevant governance mechanisms. Methods: A mixed methods approach was used to collect data in three Kenyan counties (Nairobi, Kiambu, and Kajiado). Focus group discussions (n = 23), individual interviews (n = 148), and key informant interviews (n = 10) were conducted. Results: The key actors identified include primary wholesalers, secondary wholesalers, retailers, animal health service providers (AHSPs), and farmers. Kenya imports 100% of its veterinary antibiotics: primary wholesalers legally import antibiotics as finished pharmaceutical products (90%) or active pharmaceutical ingredients (10%) after approval by the Veterinary Medicines Directorate. Secondary wholesalers play a major role in the distribution of antibiotics (60% of antibiotics) from importers to farmers, AHSPs, and retailers. Some of the illegal sources of antibiotics include unlicenced/unauthorized middlemen and online platforms that sell directly to retailers, AHSPs, and farmers. Discussion: Despite the presence of various laws and regulations governing the antibiotic value chain, implementation has been a challenge due to financial and human resource constraints. This contributes to over-the-counter sale of antibiotics without prescription, unlicensed businesses selling antibiotics, illegal importation, and presence of poor-quality drugs. There is a need to review the applicability of existing policies and address policy gaps (e.g., product containing antibiotic combinations, and use of human critically important antibiotics) to ensure the prudent sale and use of antibiotics, pharmacovigilance, antimicrobial use surveillance, and developing a business model that aligns with antibiotic stewardship. Additional interventions include awareness raising and capacity building of the different stakeholders along the antibiotic distribution chain to reduce antibiotic mis- and overuse.

Antibiotic prescribing practices in community and clinical settings during the COVID-19 pandemic in Nairobi, Kenya.

The COVID-19 pandemic has significantly impacted healthcare systems, including antibiotic use practices. We present data on patterns of antibiotic dispensing and use in community and hospital settings respectively in Nairobi, Kenya during the pandemic. We conducted interviews with 243 pharmacies in Nairobi using a standardised questionnaire from November to December 2021. The data collected included demographic characteristics, antibiotic customers, types of antibiotics sold, and antibiotic prescribing practices. Additionally, we retrospectively reviewed health records for 992 and 738 patients admitted in COVID-19 and general wards at two large inpatient hospitals between April 2020 and May 2021, and January 2019 to October 2021, respectively. Demographic, utilisation of laboratory services, treatment, clinical, and outcome data were collected using a modified Global WHO Point Prevalence Surveys (Global-PPS) tool. Almost all pharmacies (91.4%) served customers suspected of having COVID-19 with a mean weekly number of 15.6 customers. All pharmacies dispensed antibiotics, mainly azithromycin and beta lactams to suspected COVID-19 infected customers. 83.4% of hospitalised COVID-19 patients received at least one antibiotic at some point during their hospitalisation, which was significantly higher than the 53.8% in general ward patients (p<0.001). Similarly, the average number of antibiotics administered to COVID-19 patients was higher than that of patients in the general ward (1.74 vs 0.9). Azithromycin and ceftriaxone were the most commonly used antibiotics in COVID-19 patients compared to ceftriaxone and metronidazole in the general wards. Only 2% of antibiotic prescriptions for COVID-19 patients were supported by microbiological investigations, which was consistent with the proportion of 6.8% among the general ward population. Antibiotics were commonly prescribed to customers and patients suspected of having COVID-19 either in community pharmacies or in hospital, without a prescription or laboratory diagnosis. These findings emphasize the crucial role of antibiotic stewardship, particularly in community pharmacies, in the context of COVID-19.

Navigating One Health in research-for-development: Reflections on the design and implementation of the CGIAR Initiative on One Health.

Adopting One Health approaches is key for addressing interconnected health challenges. Yet, how to best put One Health into practice in research-for-development initiatives aiming to 'deliver impacts' remains unclear. Drawing on the CGIAR Initiative on One Health - a global initiative to address zoonotic diseases, antimicrobial resistance, and food and water safety - we reflect on challenges during program conception and implementation, prompting us to suggest improvements in multisectoral collaboration, coordination, and communication. Our approach involves conducting a researcher-centered process evaluation, comprising individual interviews that are subsequently thematically analyzed and synthesized. The key takeaway is that limited time for planning processes and short program timelines compared to envisioned development impacts may impede research-for-development efforts. Yet, collaborative work can be successful when adequate time and resources are allocated for planning with minimal disruption throughout implementation. Additionally, due to the multifaceted nature of One Health initiatives, it is important to pay attention to co-benefits and trade-offs, where taking action in one aspect may yield advantages and disadvantages in another, aiding to identify sustainable One Health development pathways. Forming close partnerships with national governments and local stakeholders is essential not only to promote sustainability but also to ensure local relevance, enhancing the potential for meaningful impact. Finally, regularly assessing progress toward development goals is critical as development stands as an overarching objective.

Understanding the role of household hygiene practices and foodborne disease risks in child stunting: a UKRI GCRF Action Against Stunting Hub protocol paper.

INTRODUCTION: Environmental hygiene and food safety are important determinants of child stunting. This research aims to explore the relationship between child stunting and household hygiene practices and behaviours, including the availability of water, sanitation and hygiene (WASH) facilities; the use of safe food and good quality drinking water (especially when used for complementary feeding); hygienic practices in food transport, storage and preparation and the control of cross-contamination from animals, their produce and waste. METHODS AND ANALYSIS: This study is part of a wider observational study which aims to investigate the interdisciplinary factors contributing to child stunting using a 'whole child' paradigm. The observational study recruits women during pregnancy in Hyderabad, India, Lombok, Indonesia and Kaffrine, Senegal, and dyads (ie, 500 mother-infant pairs per country) are followed longitudinally up to 24 months after birth. Within the interdisciplinary niche, the study here has developed tools to investigate the potential exposure pathways to environmental pathogen contamination of foods and water. Holistic WASH and food safety data collection tools have been developed to explore exposure pathways at the household level, including: (1) survey questionnaires; (2) spot-checks; (3) biological sampling of drinking water, food and domestic surfaces and (4) direct observation. An integrated analytical approach will be used to triangulate the evidence in order to examine the relationships between child stunting, WASH and food safety behaviours. ETHICS AND DISSEMINATION: Ethical approval of the study was granted by the ethics committee of the LSHTM, RVC, ILRI, ICMR, IIPHG, SEAMEO-RECFON, University of Cheikh Anta Diop. Findings of the study will be disseminated through publication in peer-reviewed journals, relevant international conferences, public engagement events, and policy-maker and stakeholder events.

Fate and transport modelling for evaluating antibiotic resistance in aquatic environments: Current knowledge and research priorities.

Antibiotics have revolutionised medicine in the last century and enabled the prevention of bacterial infections that were previously deemed untreatable. However, in parallel, bacteria have increasingly developed resistance to antibiotics through various mechanisms. When resistant bacteria find their way into terrestrial and aquatic environments, animal and human exposures increase, e.g., via polluted soil, food, and water, and health risks multiply. Understanding the fate and transport of antibiotic resistant bacteria (ARB) and the transfer mechanisms of antibiotic resistance genes (ARGs) in aquatic environments is critical for evaluating and mitigating the risks of resistant-induced infections. The conceptual understanding of sources and pathways of antibiotics, ARB, and ARGs from society to the water environments is essential for setting the scene and developing an appropriate framework for modelling. Various factors and processes associated with hydrology, ecology, and climate change can significantly affect the fate and transport of ARB and ARGs in natural environments. This article reviews current knowledge, research gaps, and priorities for developing water quality models to assess the fate and transport of ARB and ARGs. The paper also provides inputs on future research needs, especially the need for new predictive models to guide risk assessment on AR transmission and spread in aquatic environments.

Antibiotic quality and use practices amongst dairy farmers and drug retailers in central Kenyan highlands.

Understanding antibiotic use in dairy systems is critical to guide antimicrobial stewardship programs. We investigated antibiotic use practices in small-holder dairy farms, antibiotic quality, and antimicrobial resistance (AMR) awareness among veterinary drug retailers in a mixed farming community in the central Kenyan highlands. Data were collected from 248 dairy farms and 72 veterinary drug stores between February 2020 and October 2021. A scale was developed to measure knowledge about AMR and antibiotic use using item response theory, and regression models were used to evaluate factors associated with antibiotic use and AMR knowledge. The active pharmaceutical ingredient (API) content of 27 antibiotic samples was determined using high-performance liquid chromatography (HPLC). The presence and levels of 11 antibiotic residues in 108 milk samples collected from the study farms were also investigated using liquid chromatography tandem mass spectrometry (LC-MS/MS). Almost all farms (98.8%, n = 244) reported using antibiotics at least once in the last year, mostly for therapeutic reasons (35.5%). The most used antibiotics were tetracycline (30.6%), penicillin (16.7%), and sulfonamide (9.4%), either individually or in combination, and predominantly in the injectable form. Larger farm size (OR = 1.02, p < 0.001) and history of vaccination use (OR = 1.17, p < 0.001) were significantly associated with a higher frequency of antibiotic use. Drug retailers who advised on animal treatments had a significantly higher mean knowledge scores than those who only sold drugs. We found that 44.4% (12/27) of the tested antibiotics did not meet the United States Pharmacopeial test specifications (percentage of label claim). We detected nine antibiotics in milk, including oxytetracycline, sulfamethoxazole, and trimethoprim. However, only three samples exceeded the maximum residue limits set by the Codex Alimentarius Commission. Our findings indicate that antibiotics of poor quality are accessible and used in small-holder dairy systems, which can be found in milk. These results will aid future investigations on how to promote sustainable antibiotic use practices in dairy systems.

Practices and drivers for antibiotic use in cattle production systems in Kenya.

Understanding antibiotic use in livestock systems is key in combating antimicrobial resistance (AMR) and developing effective interventions. Using a standardised questionnaire, we investigated the patterns and drivers of antibiotic use in 165 cattle farms across the three major cattle production systems in Kenya: intensive, extensive, and semi-intensive systems across in three counties: Machakos, Makueni and Narok in Kenya. We used a causal diagram to inform regression models to explore the drivers of antibiotic use in the study farms. Antibiotic use was reported in 92.7% of farms, primarily for prophylactic purposes. Oxytetracycline, penicillin, and streptomycin were the most used antibiotics to treat and control the most reported diseases including mastitis, diarrhoea and East Coast fever (ECF). Regression analysis indicated a positive association between the frequency of antibiotic use at the farm level and both disease incidence and herd size. Conversely, farms that provided cattle with appropriate housing were less likely to use antibiotics, and there was no difference in antibiotic use between those who consulted with veterinarians or sourced antibiotics directly from animal health providers. Our study highlights the complexities around understanding the interplay between practices and drivers of antibiotic use. It also underscores the necessity to enhance education regarding the appropriate usage of antibiotics among cattle farmers, encourage the adoption of proper herd management practices which may reduce disease burden, and reinforce veterinary services and supportive legislation to promote the prudent use of antimicrobials.

Risk factors for diarrheagenic Escherichia coli infection in children aged 6-24 months in peri-urban community, Nairobi, Kenya.

Escherichia coli commonly inhabits the gut of humans and animals as part of their microbiota. Though mostly innocuous, some strains have virulence markers that make them pathogenic. This paper presents results of a cross-sectional epidemiological study examining prevalence of diarrheagenic E. coli (DEC) pathotypes in stool samples of asymptomatic healthy children (n = 540) in Dagoretti South subcounty, Nairobi, Kenya. E. coli was cultured and pathotyped using PCR to target specific virulence markers associated with Shiga-toxin, enteropathogenic, enterotoxigenic, enteroaggregative, entero-invasive and diffusely adherent E. coli. Overall prevalence of DEC pathotypes was 20.9% (113/540) with enteropathogenic E. coli being the most prevalent (34.1%), followed by enteroaggregative E. coli (23.5%) and Shiga-toxin producing E. coli (22.0%) among positive samples. We found evidence of co-infection with multiple pathotypes in 15% of the positive samples. Our models indicated that at the household level, carriage of DEC pathotypes in children was associated with age group [12-18 months] (OR 1.78; 95%CI 1.03-3.07; p = 0.04), eating matoke (mashed bananas) (OR 2.32; 95%CI 1.44-3.73; p = 0.001) and pulses/legumes (OR 1.74; 95%CI 1.01-2.99; p = 0.046) while livestock ownership or contact showed no significant association with DEC carriage (p>0.05). Our findings revealed significant prevalence of pathogenic DEC circulating among presumptive healthy children in the community. Since there has been no previous evidence of an association between any food type and DEC carriage, unhygienic handling, and preparation of matoke and pulses/legumes could be the reason for significant association with DEC carriage. Children 12-18 months old are more prone to DEC infections due to exploration and hand-to-mouth behavior. A detailed understanding is required on what proportion of positive cases developed severe symptomatology as well as fatal outcomes. The co-infection of pathotypes in the rapidly urbanizing environment needs to be investigated for hybrid or hetero-pathotype circulation that have been implicated in previous infection outbreaks.

Prevalence and risk factors associated with the occurrence of Campylobacter sp. in children aged 6-24 months in peri-urban Nairobi, Kenya.

Introduction: Campylobacter bacteria is a major cause of foodborne-related bacterial gastroenteritis in humans worldwide. It is known to cause diarrhea in young children which has been shown to directly affect their weight and height as a result of malnutrition. Severe cases of diarrhea can also lead to death. Most of the burden is experienced in resource-limited countries in Africa and Southeast Asia where the disease is linked to poor hygiene and sanitation. The objective of this study was to determine the prevalence of Campylobacter in children aged between 6 and 24 months in Nairobi, Kenya and identify potential risk factors associated with their occurrence. Methods: A cross-sectional study was carried out between May to December 2021. A total of 585 randomly selected households were visited in two wards (Uthiru/Ruthimitu and Riruta) in Dagoretti South sub-county, Nairobi. A questionnaire regarding how children's food is handled, the major foods consumed, sanitation and hygiene, and animal ownership was conducted among caregivers to identify associated risk factors. Stool samples were collected from 540/585 children and screened for the presence of Campylobacter using culture-based methods and confirmed through PCR. Results: Of the 540 children's stool samples processed, Campylobacter isolates were detected in 4.8% (26/540). Campylobacter jejuni (C. jejuni) was the most common species in 80.8% of positive samples compared to Campylobacter coli (C. coli) in 26.9% of samples. In six samples, both C. jejuni and C. coli were isolated, while in four samples, it was not possible to speciate the Campylobacter. Drinking cow's milk (OR 4.2, 95% CI 1.4 - 12.6) and the presence of animal feces in the compound (OR 3.4, 95% CI 1.1 - 10.3) were found to be statistically associated with Campylobacter carriage in children. Discussion: The carriage of Campylobacter in children in this community indicates a need for further investigation on source attribution to understand transmission dynamics and inform where to target interventions. Awareness creation among caregivers on good personal and food hygiene is needed, including boiling milk before consumption. Implementation of biosecurity measures at the household level is highly recommended to reduce contact between animals and humans.

Biosecurity and water, sanitation, and hygiene (WASH) interventions in animal agricultural settings for reducing infection burden, antibiotic use, and antibiotic resistance: a One Health systematic review.

Prevention and control of infections across the One Health spectrum is essential for improving antibiotic use and addressing the emergence and spread of antibiotic resistance. Evidence for how best to manage these risks in agricultural communities-45% of households globally-has not been systematically assembled. This systematic review identifies and summarises evidence from on-farm biosecurity and water, sanitation, and hygiene (WASH) interventions with the potential to directly or indirectly reduce infections and antibiotic resistance in animal agricultural settings. We searched 17 scientific databases (including Web of Science, PubMed, and regional databases) and grey literature from database inception to Dec 31, 2019 for articles that assessed biosecurity or WASH interventions measuring our outcomes of interest; namely, infection burden, microbial loads, antibiotic use, and antibiotic resistance in animals, humans, or the environment. Risk of bias was assessed with the Systematic Review Centre for Laboratory Animal Experimentation tool, Risk of Bias in Non-Randomized Studies of Interventions, and the Appraisal tool for Cross-Sectional Studies, although no studies were excluded as a result. Due to the heterogeneity of interventions found, we conducted a narrative synthesis. The protocol was pre-registered with PROSPERO (CRD42020162345). Of the 20 672 publications screened, 104 were included in this systematic review. 64 studies were conducted in high-income countries, 24 studies in upper-middle-income countries, 13 studies in lower-middle-income countries, two in low-income countries, and one included both upper-middle-income countries and lower-middle-income countries. 48 interventions focused on livestock (mainly pigs), 43 poultry (mainly chickens), one on livestock and poultry, and 12 on aquaculture farms. 68 of 104 interventions took place on intensive farms, 22 in experimental settings, and ten in smallholder or subsistence farms. Positive outcomes were reported for ten of 23 water studies, 17 of 35 hygiene studies, 15 of 24 sanitation studies, all three air-quality studies, and 11 of 17 other biosecurity-related interventions. In total, 18 of 26 studies reported reduced infection or diseases, 37 of 71 studies reported reduced microbial loads, four of five studies reported reduced antibiotic use, and seven of 20 studies reported reduced antibiotic resistance. Overall, risk of bias was high in 28 of 57 studies with positive interventions and 17 of 30 studies with negative or neutral interventions. Farm-management interventions successfully reduced antibiotic use by up to 57%. Manure-oriented interventions reduced antibiotic resistance genes or antibiotic-resistant bacteria in animal waste by up to 99%. This systematic review highlights the challenges of preventing and controlling infections and antimicrobial resistance, even in well resourced agricultural settings. Most of the evidence emerges from studies that focus on the farm itself, rather than targeting agricultural communities or the broader social, economic, and policy environment that could affect their outcomes. WASH and biosecurity interventions could complement each other when addressing antimicrobial resistance in the human, animal, and environmental interface.

Isolation and Characterization of a Novel Phage Collection against Avian-Pathogenic Escherichia coli.

The increase in antibiotic-resistant avian-pathogenic Escherichia coli (APEC), the causative agent of colibacillosis in poultry, warrants urgent research and the development of alternative therapies. This study describes the isolation and characterization of 19 genetically diverse, lytic coliphages, 8 of which were tested in combination for their efficacy in controlling in ovo APEC infections. Genome homology analysis revealed that the phages belong to nine different genera, one of them being a novel genus (Nouzillyvirus). One phage, REC, was derived from a recombination event between two Phapecoctavirus phages (ESCO5 and ESCO37) isolated in this study. Twenty-six of the 30 APEC strains tested were lysed by at least one phage. Phages exhibited varying infectious capacities, with narrow to broad host ranges. The broad host range of some phages could be partially explained by the presence of receptor-binding protein carrying a polysaccharidase domain. To demonstrate their therapeutic potential, a phage cocktail consisting of eight phages belonging to eight different genera was tested against BEN4358, an APEC O2 strain. In vitro, this phage cocktail fully inhibited the growth of BEN4358. In a chicken lethality embryo assay, the phage cocktail enabled 90% of phage-treated embryos to survive infection with BEN4358, compared with 0% of nontreated embryos, indicating that these novel phages are good candidates to successfully treat colibacillosis in poultry. IMPORTANCE Colibacillosis, the most common bacterial disease affecting poultry, is mainly treated by antibiotics. Due to the increased prevalence of multidrug-resistant avian-pathogenic Escherichia coli, there is an urgent need to assess the efficacy of alternatives to antibiotherapy, such as phage therapy. Here, we have isolated and characterized 19 coliphages that belong to nine phage genera. We showed that a combination of 8 of these phages was efficacious in vitro to control the growth of a clinical isolate of E. coli. Used in ovo, this phage combination allowed embryos to survive APEC infection. Thus, this phage combination represents a promising treatment for avian colibacillosis.

Antimicrobial Use by Peri-Urban Poultry Smallholders of Kajiado and Machakos Counties in Kenya.

Antimicrobial use (AMU) is a major driver of antimicrobial resistance (AMR). An understanding of current practices can lead to better targeting of AMU-reducing interventions. An analysis of the distribution and current usage of veterinary drugs in peri-urban smallholder poultry systems in Kenya was undertaken. A survey among poultry farmers and key informant interviews with agrovet operators and other players in the value chain was conducted in Machakos and Kajiado counties. Interview data were analyzed using descriptive and thematic approaches. A total of 100 farmers were interviewed. The majority (58%) were > 50 years old, and all kept chickens, while 66% kept other livestock. Antibiotics constituted 43% of the drugs reportedly used on the farms (n = 706). These were mostly administered by the farmers themselves (86%) through water (98%). Leftover drugs were stored for later use (89%) or disposed of (11%). Incineration was the main method for the disposal of leftover drugs and empty containers. As described by the key informants (n = 17), the drug distribution chain relied on agrovet shops that were supplied by local distributors and pharmaceutical companies, which, in turn, supplied drugs to the farmers. Farmers reportedly purchased drugs without prescriptions and rarely observed the withdrawal periods. Drug quality was a concern, especially for products requiring reconstitution.

Drug Combination of Ciprofloxacin and Polymyxin B for the Treatment of Multidrug-Resistant Acinetobacter baumannii Infections: A Drug Pair Limiting the Development of Resistance.

Polymyxins are considered as last-resort antibiotics to treat infections caused by Acinetobacter baumannii. However, there are increasing reports of resistance in A. baumannii to polymyxins. In this study, inhalable combinational dry powders consisting of ciprofloxacin (CIP) and polymyxin B (PMB) were prepared by spray-drying. The obtained powders were characterized with respect to the particle properties, solid state, in vitro dissolution and in vitro aerosol performance. The antibacterial effect of the combination dry powders against multidrug-resistant A. baumannii was assessed in a time-kill study. Mutants from the time-kill study were further investigated by population analysis profiling, minimum inhibitory concentration testing, and genomic comparisons. Inhalable dry powders consisting of CIP, PMB and their combination showed a fine particle fraction above 30%, an index of robust aerosol performance of inhaled dry powder formulations in the literature. The combination of CIP and PMB exhibited a synergistic antibacterial effect against A. baumannii and suppressed the development of CIP and PMB resistance. Genome analyses revealed only a few genetic differences of 3-6 SNPs between mutants and the progenitor isolate. This study suggests that inhalable spray-dried powders composed of the combination of CIP and PMB is promising for the treatment of respiratory infections caused by A. baumannii, and this combination can enhance the killing efficiency and suppress the development of drug resistance.

Knowledge, Attitudes, and Practices Related to Antibiotic Use and Antibiotic Resistance among Poultry Farmers in Urban and Peri-Urban Areas of Ouagadougou, Burkina Faso.

Increased use of antibiotics in livestock is a public health concern, as it poses risks of antibiotic residues and antibiotic-resistant pathogens entering the food chains and infecting humans. A cross-sectional survey was conducted on 216 poultry farms to study knowledge, attitudes and practices of poultry farmers on the use of antibiotics in urban and peri-urban areas of Ouagadougou. Results show that only 17.13% (37/216) of farmers attended training on poultry production. Majority of farmers-85.65% (185/216) were not knowledgeable about the rational use of antibiotics. When there was a disease outbreak, 31.98% (63/197) of farmers used veterinary drugs without a prescription and 22.34% (44/197) consulted a community animal health worker. It should also be noted that 79.19% (156/197) of farmers reported using chicken meat as per normal if the bird died during or right after treatment with an antibiotic. Knowledge of rational use of antibiotics was positively influenced by a good attitude adopted by the farmer during the illness of birds and negatively influenced by disease treatment success and high level of education of the farmer. Lack of knowledge about the rational use of antibiotics including their use without a prescription are serious risk factors for the emergence of antimicrobial resistance. Awareness of farmers and other veterinary drug supply chain actors such as drug stockists and animal health workers on best practices in antimicrobial use and promotion of good biosecurity on farms are important to reduce the misuse of antibiotics.

Presence of Methicillin Resistant Staphylococcus aureus (MRSA) in Feces of the Small Indian Mongooses (Urva auropunctata) on Saint Kitts and Nevis, West Indies.

Although, historically, Methicillin-Resistant Staphylococcus aureus (MRSA) was restricted to humans, since 2005 these strains emerged in livestock and wildlife. Therefore, a One Health approach was applied to analyze the diversity and characteristics of S. aureus strains isolated from the invasive species of mongoose (Urva auropunctata) in St. Kitts. Fecal samples collected from these animals (n = 81) were cultured on selective agar. The isolated S. aureus strains were identified using MALDI-TOF and further characterized by whole genome sequence analysis. The fecal microbiome study identified the presence of S. aureus in 5 animals. Both MSSA (n = 3) and MRSA (n = 2) strains were identified. The two MRSA isolated were nearly identical ST5 SCCmec IVa (2B) strains. The two MSSA isolated were a new ST7434, pertaining to clonal complex 30, and the other belonged to ST5, but unrelated to the MRSA ST5. The SCCmec IVa (2B) is, however, the main SCCmec in human MRSA of different STs identified in St Kitts, indicating potential horizontal transmission events. In conclusion, a new type of MSSA, ST7434, was found and MRSA ST5 t002 SCCmec IVa (2B) found its way into wildlife on a small Caribbean Island. Further One Health studies are necessary to determine the role of MRSA in wildlife.

Antimicrobial Resistance in Africa-How to Relieve the Burden on Family Farmers.

Although currently available data indicate that Africa has the lowest usage of antimicrobials in animals in the world (adjusted by animal biomass), data show a high prevalence of antimicrobial resistance in foodborne pathogens isolated from animals and animal products. Apart from the lack of solid data on antimicrobial use in many countries in Africa, different hypotheses could explain this situation. Qualitative interviews of farmers show a lack of knowledge and uninformed use of antimicrobials. Considering the development of animal farming to meet an increasing demand for proteins, this deficiency represents a serious public health issue. We advocate for policies that consider the specific challenges faced by family farmers in Africa, to simultaneously improve access to veterinary drugs while strengthening the regulation of their use. We propose a global approach targeting the agri-food system, offering innovative social and technical interventions on antimicrobial usage, adapted to family farmers.

Methicillin-Resistant and Methicillin-Susceptible Staphylococcus from Vervet Monkeys (Chlorocebus sabaeus) in Saint Kitts.

Antimicrobial resistance has been described in all ecosystems, including wildlife. Here we investigated the presence of methicillin-resistant and susceptible staphylococci in both colony-born and wild vervet monkeys (Chlorocebus sabaeus). Through selective isolation, PCR, MALDI-TOF, and whole-genome sequencing, methicillin-resistant and susceptible Staphylococcus spp. isolated from vervet monkeys were characterized. We obtained putatively methicillin-resistant staphylococci from 29 of the 34 nasal samples collected. Strains were identified by MALDI-TOF analysis. Staphylococcus cohnii (n = 15) was the most commonly isolated species, while nine other species were isolated one or two times. PCR analysis indicated that eight [28%] strains were mecA positive. The whole-genome sequencing [WGS] included eight methicillin-resistant strains (S. epidermidis (n = 2), S. cohnii (n = 3), S. arlettae (n = 2) and S. hominis (n = 1)), nine additional S. cohnii strains and two strains that could not be identified by MALDI-TOF, but genetically characterized as one S. cohnii and one S. warneri. Different resistance genes carried by different mobile genetic elements, mainly blaZ (n = 10) and tet(K) (n = 5) were found, while msr(A), cat, fosB, dfrG, erm(C), mph(C) and str were identified in one to three strains. Phylogenetic analysis of the S. cohnii strains based on SNPs indicated four clusters associated with colony born or wild. In addition, one singleton S. cohnii isolated did not form a separate group and clustered within other S. cohnii strains submitted to the NCBI. In this study, we demonstrated the presence of AMR and mobile genetic elements to both colony-born and wild vervet monkeys. We also identified a previously undescribed prevalence of S. cohnii in the nasal flora of these monkeys, which merits further investigation.

One Health Genomic Study of Human and Animal Klebsiella pneumoniae Isolated at Diagnostic Laboratories on a Small Caribbean Island.

Klebsiella pneumoniae causes a variety of infections in both humans and animals. In this study, we characterised the genomes of human and animal isolates from two diagnostic laboratories on St. Kitts, a small Caribbean island inhabited by a large population of vervet monkeys. In view of the increased chances of direct or indirect contact with humans and other animal species, we used the One Health approach to assess transmission of K. pneumoniae across host species by sequencing 82 presumptive K. pneumoniae clinical isolates from humans (n = 51), vervets (n = 21), horses (n = 5), dogs (n = 4) and a cat (n = 1). Whole genome sequencing (WGS) was carried out using Illumina technology. De novo assembly was performed in CLC Genomics Workbench v.11.0. Single nucleotide polymorphisms were detected using NASP followed by phylogenetic analysis using IQ-TREE. Virulence and antimicrobial resistance gene contents were analysed using the Kleborate and CGE pipelines. WGS-based analysis showed that 72 isolates were K. pneumoniae sensu stricto and five K. quasipneumoniae and five K. variicola. K. pneumoniae isolates belonged to 35 sequence types (ST), three of which were occasionally shared between humans and animals: ST23, ST37 and ST307. The ST23 strains from vervets formed a separate cluster amongst publicly available sequenced ST23 strains, indicating the presence of a specific vervet sublineage. Animal strains harbored fewer resistance genes and displayed distinct virulence traits that appeared to be host-specific in vervet isolates. Our results show that K. pneumoniae infections on this Caribbean island are usually caused by host-specific lineages.

New insights into the biodiversity of coliphages in the intestine of poultry.

Despite phages' ubiquitous presence and great importance in shaping microbial communities, little is known about the diversity of specific phages in different ecological niches. Here, we isolated, sequenced, and characterized 38 Escherichia coli-infecting phages (coliphages) from poultry faeces to gain a better understanding of the coliphage diversity in the poultry intestine. All phages belonged to either the Siphoviridae or Myoviridae family and their genomes ranged between 44,324 and 173,384 bp, with a G+C content between 35.5 and 46.4%. Phylogenetic analysis was performed based on single "marker" genes; the terminase large subunit, portal protein, and exonucleases, as well as the full draft genomes. Single gene analysis resulted in six distinct clusters. Only minor differences were observed between the different phylogenetic analyses, including branch lengths and additional duplicate or triplicate subclustering. Cluster formation was according to genome size, G+C content and phage subfamily. Phylogenetic analysis based on the full genomes supported these clusters. Moreover, several of our Siphoviridae phages might represent a novel unclassified phage genus. This study allowed for identification of several novel coliphages and provides new insights to the coliphage diversity in the intestine of poultry. Great diversity was observed amongst the phages, while they were isolated from an otherwise similar ecosystem.