Antimicrobial Resistance Profiles Diversity in Salmonella from Humans Cattle, 2004-2011

Analysis of long-term anti-microbial resistance (AMR) data is useful to understsource transmission dynamics of AMR. We analysed 5124 human clinical isolates from Washington State Department of Health, 391 cattle clinical isolates from the Washington Animal Disease Diagnostic Laboratory 1864 non-clinical isolates from foodborne disease research on dairies in the Pacific Northwest. Isolates were assigned profiles based on phenotypic resistance to 11 anti-microbials belonging to eight classes. Salmonella Typhimurium (ST), Salmonella Newport (SN) Salmonella Montevideo (SM) were the most common serovars in both humans cattle. Multinomial logistic regression showed ST SN from cattle had greater probability of resistance to multiple classes of anti-microbials than ST SN from humans (P < 0.0001). While these findings could be consistent with the belief that cattle are a source of resistant ST SN for people, occurrence of profiles unique to cattle not observed in temporally related human isolates indicates these profiles are circulating in cattle only. We used various measures to assess AMR diversity, conditional on the weighting of rare versus abundant profiles. AMR profile richness was greater in the common serovars from humans, although both source data sets were dominated by relatively few profiles. The greater profile richness in human Salmonella may be due to greater diversity of sources entering the human population compared to cattle or due to continuous evolution in the human environment. Also, AMR diversity was greater in clinical compared to non-clinical cattle Salmonella, this could be due to anti-microbial selection pressure in diseased cattle that received treatment. The use of bootstrapping techniques showed that although there were shared profiles between humans cattle, the expected observed number of profiles was different, suggesting Salmonella associated resistance from humans cattle may not be wholly derived from a common population

Salmonella in Wild Birds Utilizing Protected and Human Impacted Habitats, Uganda

As human populations in Africa expand, humans encroach and modify wildlife habitats for farming, fishing, tourism, or settlement. Anthropogenic activities in shared environments may promote transmission of zoonotic pathogens between humans, domestic animals, and wildlife. Between July 2012 and February 2014, we evaluated Salmonella prevalence, serovars, genotypes, and antibiotic resistant phenotypes in resident and migratory birds utilizing human-impacted habitats in northwestern Lake Victoria and protected habitats in Queen Elisabeth National Park. Salmonella occurrence in the urban environment was assessed by sampling storm-water and wastewater from a channel that drains Kampala City into Lake Victoria. Salmonella was detected in 4.3% pooled bird fecal samples, and 57.1% of environmental samples. While birds in impacted and protected areas shared serovars, the genotypes were distinct. We found distinct strains in birds and the environment suggesting some strains in birds are host adapted, and strains circulating in the environment may not necessarily disseminate to birds. Conversely, birds in both impacted and protected areas shared strains with the urban environment, suggesting Salmonella disseminates between impacted environments and birds across sites. Overall, more strains were observed in the urban environment compared to birds, and poses risk of Salmonella reemergence in birds and transmission across species and space

Antimicrobial Resistance Diversity Suggestive of Distinct Salmonella Typhimurium Sources or Selective Pressures in Food-Production Animals

Salmonella enterica subsp. enterica serovar Typhimurium is a common cause of enterocolitis in humans globally, with multidrug resistant (MDR) strains posing an enhanced threat. S. Typhimurium is also a pathogen in food-production animals, and these populations can act as reservoirs of the bacterium. Therefore, surveillance and control measures within food-production animal populations are of importance both to animal and human health and have the potential to be enhanced though improved understanding of the epidemiology of S. Typhimurium within and between food-production animal populations. Here, data from Scotland and national surveillance England and Wales data for isolates from cattle (n = 1115), chickens (n = 248) and pigs (n = 2174) collected between 2003 and 2014 were analyzed. Ecological diversity analyses and rarefaction curves were used to compare the diversity of observed antimicrobial resistance (AMR) profiles between the host species, and within host species populations. Higher AMR profile diversity was observed in isolates from pigs compared to chickens across diversity measures and isolates from cattle for three of four diversity measures. Variation in AMR profile diversity between production sectors was noted, with higher AMR diversity of isolates from broiler compared to layer chickens, breeder compared to rearer and finisher pigs and beef compared to dairy cattle. Findings indicate variation in AMR profile diversity both within and between food-production animal host species. These observations suggest alternate sources of AMR bacteria and/or variation in selective evolutionary pressures within and between food-production animal host species populations

Prevalence, antimicrobial susceptibility and risk factors associated with non-typhoidal Salmonella on Ugandan layer hen farms

Abstract Background Non-typhoidal Salmonella (NTS) are among the leading global foodborne pathogens and a significant public health threat. Their occurrence in animal reservoirs and their susceptibilities to commonly used antimicrobials are poorly understood in developing countries. The aim of this study was to estimate the prevalence, determine antimicrobial susceptibility and identify risk factors associated with NTS presence in laying hen farms in Uganda through a cross-sectional study. Results Pooled faecal samples were collected from 237 laying hen farms and these were analysed for NTS following standard laboratory procedures. In total, 49 farms (20.7%; 95% Confidence interval (CI): 15.6–25.6%) were positive for NTS presence. Altogether, ten Salmonella serotypes were identified among the confirmed 78 isolates, and the predominant serotypes were Salmonella Newport (30.8%), S. Hadar (14.1%), S. Aberdeen (12.8%), S. Heidelberg (12.8%), and S. Bolton (12.8%). Phenotypic antimicrobial resistance was detected in 45(57.7%) of the isolates and the highest resistance was against ciprofloxacin (50.0%) followed by sulphonamides (26.9%) and sulphamethoxazole/trimethoprim (7.7%). Resistance was significantly associated with sampled districts (p = 0.034). Resistance to three or more drugs, multi-drug resistance (MDR) was detected in 12 (15.4%) of the isolates, 9 (75%) of these were from Wakiso district. A multivariable logistic model identified large farm size (OR = 7.0; 95% CI: 2.5–19.8) and the presence of other animal species on the farm (OR = 5.9; 95% CI: 2.1–16.1) as risk factors for NTS prevalence on farms. Having a separate house for birds newly brought to the farms was found to be protective (OR = 0,4; 95% CI: 0.2–0.8). Conclusion This study has highlighted a high prevalence and diversity of NTS species in laying hen farms in Uganda and identified associated risk factors. In addition, it has demonstrated high levels of antimicrobial resistance in isolates of NTS. This could be because of overuse or misuse of antimicrobials in poultry production. Also importantly, the insights provided in this study justifies a strong case for strengthening One Health practices and this will contribute to the development of NTS control strategies at local, national and international levels

SALMONELLA AND ANTIMICROBIAL RESISTANCE IN HUMANS, LIVESTOCK AND WILD BIRDS

Salmonella are Gram negative bacteria that are classified into over 2600 serovars. The serovars that cause typhoid fever are restricted to humans, whereas non-typhoidal Salmonella serovars (NTS) infect multiple hosts worldwide. However, fundamental differences exist between developed countries and sub-Saharan Africa with regards to sources, transmission, host and environmental risk factors, and disease outcome. In United States, although NTS are mainly foodborne, control measures implemented within slaughter and processing facilities have failed to reduce disease incidence implying transmission is not fully understood. In Africa, limited research has been done; hence NTS transmission is poorly understood. This study was conducted to better understand sources and transmission of NTS and associated antimicrobial resistance (AMR).We analyzed long-term human and cattle AMR data from Pacific Northwest using diversity measures and bootstrapping techniques. We show that some AMR profiles in the predominant serovars were common between host populations, but more profiles were unique to source populations than were shared. Also, the expected and observed number of AMR profiles in humans and cattle were different. These results suggest Salmonella and AMR from humans and cattle may not be wholly derived from a common population.We also determined phenotypic antimicrobial structure and genotypic structure of common serovars from various sources (storm-water, human wastewater, abattoir flush-water and floor swab, poultry and swine feces) in Kampala, Uganda. We found similar strains among different sources suggesting NTS disseminates amongst humans, livestock and the environment. Also, more resistance was detected in poultry suggesting poultry are potential reservoirs.Next, we assessed the risk of Salmonella shedding in water-birds utilizing impacted and conserved areas, but found no difference in prevalence by location. Some strains were distinct to birds, while other strains in birds reflected strains in the urban environment. Of concern, an important bird area close to the city attracts high bird diversity, and could favor reemergence of fecal zoonotic pathogens.Finally, we used a mathematical modeling approach to gain insights into NTS transmission. We find the proportion of humans infected via animal contact depends on assumptions of NTS prevalence in animals, and proportion of humans that contact animals

Exploring the advantages and limitations of sampling methods commonly used in research facilities for zebrafish health inspections

Examining zebrafish populations for the presence of disease is an integral component of managing fish health in research facilities. Currently, many different strategies are used for zebrafish fish health inspections, which is a scenario that may result in subjective and biased diagnostic evaluations. The goal of this study was to compare the success of pathogen detection between a sample size of randomly selected fish ( n = 60) that provides 95% confidence in pathogen detection based on a presumed pathogen prevalence level ≥5%, and other subpopulations and sample numbers commonly submitted for diagnostic testing within a 1000 tank, 30,000 fish, recirculating research system. This included fish collected from a sump tank ( n = 53), sentinel fish ( n = 11), and fish that were found moribund or freshly dead ( n = 18). Additionally, five fish from each subpopulation were collected for histopathologic examination. A second study used retrospective data to examine pathogen distribution between systems ( n = 2−5) in multi-system facilities ( n = 5) using a sample size of 60 fish per system. For the pathogens detected, results supported the use of representative sample numbers rather than smaller numbers of populations considered more at risk. The exception to this is for the moribund/mortality group, which may be a resource for targeted surveillance of select pathogens. Each system within multi-system facilities should be considered separate units in terms of fish health inspections and biosecurity. Development of these evidence-based standards for fish health inspections in zebrafish systems enhances fish welfare, provides identification of potentially zoonotic pathogens, and ensures scientific integrity and reproducibility of research results.</jats:p

Expériences sur une stratégie de dépistage de la brucellose bovine dans une zone rurale du Sud-Ouest de l'Ouganda

Quarante-trois troupeaux laitiers, comprenant 1 094 bovins, 22 moutons et 102 chèvres, ont été inclus dans une étude sérologique comparative. Le test de réaction d'agglutination (mrt), appliqué comme test de dépistage préliminaire sur des échantillons de lait de mélange, a révélé 10 % de troupeaux positifs. En raison du faible pourcentage de vaches en lactation dans les troupeaux (25 % en moyenne), de réactions faussement positives et de la mauvaise conservation du lait, le mrt a été déclaré peu satisfaisant pour détecter les troupeaux positifs. En conséquence, 756 boeufs, 22 moutons et 79 chèvres ont été examinés individuellement avec le test de Rose Bengal (rbpt), puis avec le test de fixation du complément (cffl. La correspondance entre rbpt et cft était modérée. En tenant compte des résultats du cft, la prévalence totale de l'infection à Brucella abortus était alors de 3 % (23/756). Cinquante-deux pour-cent des vaches laitières séropositives étaient âgées de plus de 6 ans. Les animaux séropositifs étaient cinq fois plus susceptibles d'avoir eu un avortement observé que les animaux séronégatifs. Le pourcentage de troupeaux infectés était de 25 % (10/40) et la prévalence de la maladie dans les troupeaux infectés variait entre 1,5 et 20,4 %, avec une moyenne de 5,6 %. Tous les taureaux de monte, les moutons et les chèvres examinés étaient séronégatifs et n'ont apparemment pas joue de rôle dans la transmission de la brucellose dans cette zone. Les tests utilisés (mrt , rbpt et cft) sont discutés et des recommandations sont données pour tenter d'approfondir la recherche sur la brucellose bovine.</jats:p

Additional file 1: of Antimicrobial use policy change in pre-weaned dairy calves and its impact on antimicrobial resistance in commensal Escherichia coli: a cross sectional and ecological study

Table S1. Antimicrobial combination treatments given to pre-weaned calves (n = 4301) on a dairy farm. Table S2. Criteria for latent class analysis model selection based on resistance to 11 antimicrobials. Table S3. Minimum inhibitory concentration (μg/ml) of antimicrobials used for agar dilution assay. (XLSX 14 kb