2021, Frentrup, Martinique, Thiel, Nadine, Junker, Vera, Behrens, Wiebke, Münch, Steffen, Siller, Paul, Kabelitz, Tina, Faust, Matthias, Indra, Alexander, Baumgartner, Stefanie, Schepanski, Kerstin, Amon, Thomas, Roesler, Uwe, Funk, Roger, Nübel, Ulrich

During a field experiment applying broiler manure for fertilization of agricultural land, we detected viable Clostridioides (also known as Clostridium) difficile in broiler faeces, manure, dust and fertilized soil. A large diversity of toxigenic C. difficile isolates was recovered, including PCR ribotypes common from human disease. Genomic relatedness of C. difficile isolates from dust and from soil, recovered more than 2 years after fertilization, traced their origins to the specific chicken farm that had delivered the manure. We present evidence of long-term contamination of agricultural soil with manure-derived C. difficile and demonstrate the potential for airborne dispersal of C. difficile through dust emissions during manure application. Clostridioides genome sequences virtually identical to those from manure had been recovered from chicken meat and from human infections in previous studies, suggesting broiler-associated C. difficile are capable of zoonotic transmission.

2020, Raafat, Dina, Mrochen, Daniel M., Al’Sholui, Fawaz, Heuser, Elisa, Ryll, René, Pritchett-Corning, Kathleen R., Jacob, Jens, Walther, Bernd, Matuschka, Franz-Rainer, Richter, Dania, Westerhüs, Uta, Pikula, Jiri, van den Brandt, Jens, Nicklas, Werner, Monecke, Stefan, Strommenger, Birgit, van Alen, Sarah, Becker, Karsten, Ulrich, Rainer G., Holtfreter, Silva

Rats are a reservoir of human- and livestock-associated methicillin-resistant Staphylococcus aureus (MRSA). However, the composition of the natural S. aureus population in wild and laboratory rats is largely unknown. Here, 144 nasal S. aureus isolates from free-living wild rats, captive wild rats and laboratory rats were genotyped and profiled for antibiotic resistances and human-specific virulence genes. The nasal S. aureus carriage rate was higher among wild rats (23.4%) than laboratory rats (12.3%). Freeliving wild rats were primarily colonized with isolates of clonal complex (CC) 49 and CC130 and maintained these strains even in husbandry. Moreover, upon livestock contact, CC398 isolates were acquired. In contrast, laboratory rats were colonized with many different S. aureus lineages-many of which are commonly found in humans. Five captive wild rats were colonized with CC398-MRSA. Moreover, a single CC30-MRSA and two CC130-MRSA were detected in free-living or captive wild rats. Rat-derived S. aureus isolates rarely harbored the phage-carried immune evasion gene cluster or superantigen genes, suggesting long-term adaptation to their host. Taken together, our study revealed a natural S. aureus population in wild rats, as well as a colonization pressure on wild and laboratory rats by exposure to livestock- and human-associated S. aureus, respectively. © 2020 by the authors.

2019, Wendt, Amanda S., Sparling, Thalia M., Waid, Jillian L., Mueller, Anna A., Gabrysch, Sabine

Introduction Chronic undernutrition affects over 150 million children worldwide and has serious consequences. The causes are complex and include insufficient dietary diversity and poor hygiene practices. Systematic reviews of nutrition-sensitive agricultural interventions concluded that while these hold promise, there is insufficient evidence for their impact on child growth. The Food and Agricultural Approaches to Reducing Malnutrition (FAARM) project is a 1:1 cluster-randomised trial aiming to evaluate the impact of a Homestead Food Production (HFP) programme implemented by Helen Keller International on women's and children's undernutrition. Methods and analysis The HFP intervention comprises training of women's groups and asset distribution to support year-round home gardening, poultry rearing and improved nutrition and hygiene practices. Formal trainings are supplemented by behaviour change communication during household visits, and facilitated links between producer groups and market actors. The FAARM trial will examine if and how this complex intervention reduces undernutrition. In 2015, FAARM enrolled married women and their children (0-3 years) in 96 rural settlements of Habiganj district in Sylhet division, Bangladesh. Covariate-constrained randomisation was used to assign 48 settlements to receive a 3-year HFP intervention, with the other 48 acting as controls, targeting over 2700 women. To study impact pathways, a surveillance system collects data on all participants every 2 months. In late 2019, children 0-3 years of age (born during the intervention period) will be surveyed, thus capturing impact during the critical first 1000 days of life. Children's length/height-for-age z-scores will be compared between intervention and control arms using mixed-effects linear regression. Secondary outcomes include women's and children's micronutrient status, dietary intake, dietary diversity and other indicators of child growth, development and morbidity. Ethics and dissemination Ethical approval was received in Bangladesh and Germany. Results will be disseminated through peer-reviewed publications and presentations in Bangladesh and internationally. Trial registration number NCT02505711; Pre-results. © Author(s) (or their employer(s)) 2019. Re-use permitted under CC BY. Published by BMJ.

2022, Aloba, B.K., Kinnevey, P.M., Monecke, S., Brennan, G.I., O'Connell, B., Blomfeldt, A., McManus, B.A., Schneider-Brachert, W., Tkadlec, J., Ehricht, R., Senok, A., Bartels, M.D., Coleman, D.C.

Background: A novel Panton–Valentine leukocidin (PVL)-positive meticillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC)5-MRSA-IVc (‘Sri Lankan’ clone) was recently described from Sri Lanka. Similar isolates caused a recent Irish hospital outbreak. Aim: To investigate the international dissemination and diversity of PVL-positive CC5-MRSA-IVc isolates from hospital and community settings using whole-genome sequencing (WGS). Methods: Core-genome single nucleotide polymorphism (cgSNP) analysis, core-genome multi-locus sequence typing (cgMLST) and microarray-based detection of antimicrobial-resistance and virulence genes were used to investigate PVL-positive CC5-MRSA-IVc (N = 214 including 46 ‘Sri Lankan’ clone) from hospital and community settings in 12 countries over 17 years. Comparators included 29 PVL-positive and 23 PVL-negative CC5/ST5-MRSA-I/II/IVa/IVc/IVg/V. Results: Maximum-likelihood cgSNP analysis grouped 209/214 (97.7%) CC5-MRSA-IVc into Clade I; average of 110 cgSNPs between isolates. Clade III contained the five remaining CC5-MRSA-IVc; average of 92 cgSNPs between isolates. Clade II contained seven PVL-positive CC5-MRSA-IVa comparators, whereas the remaining 45 comparators formed an outlier group. Minimum-spanning cgMLST analysis revealed a comparably low average of 57 allelic differences between all CC5/ST5-MRSA-IVc. All 214 CC5/ST5-MRSA-IVc were identified as ‘Sri Lankan’ clone, predominantly spa type t002 (186/214) with low population diversity and harboured a similar range of virulence genes and variable antimicrobial-resistance genes. All 214 Sri Lankan clone isolates and Clade II comparators harboured a 9616-bp chromosomal PVL-encoding phage remnant, suggesting both arose from a PVL-positive meticillin-susceptible ancestor. Over half of Sri Lankan clone isolates were from infections (142/214), and where detailed metadata were available (168/214), most were community associated (85/168). Conclusions: Stable chromosomal retention of pvl may facilitate Sri-Lankan clone dissemination.

2021, Earls, Megan R., Steinig, Eike J., Monecke, Stefan, Samaniego Castruita, José A., Simbeck, Alexandra, Schneider-Brachert, Wulf, Vremerǎ, Teodora, Dorneanu, Olivia S., Loncaric, Igor, Bes, Michèle, Lacoma, Alicia, Prat Aymerich, Cristina, Wernery, Ulrich, Armengol-Porta, Marc, Blomfeldt, Anita, Duchene, Sebastian, Bartels, Mette D., Ehricht, Ralf, Coleman, David C.

This study investigated the evolution and epidemiology of the community-associated and multidrug-resistant Staphylococcus aureus clone European CC1-MRSA-IV. Whole-genome sequences were obtained for 194 European CC1-MRSA-IV isolates (189 of human and 5 of animal origin) from 12 countries, and 10 meticillin-susceptible precursors (from North-Eastern Romania; all of human origin) of the clone. Phylogenetic analysis was performed using a maximum-likelihood approach, a time-measured phylogeny was reconstructed using Bayesian analysis, and in silico microarray genotyping was performed to identify resistance, virulence-associated and SCCmec (staphylococcal cassette chromosome mec) genes. Isolates were typically sequence type 1 (190/204) and spa type t127 (183/204). Bayesian analysis indicated that European CC1-MRSA-IV emerged in approximately 1995 before undergoing rapid expansion in the late 1990s and 2000s, while spreading throughout Europe and into the Middle East. Phylogenetic analysis revealed an unstructured meticillin-resistant S. aureus (MRSA) population, lacking significant geographical or temporal clusters. The MRSA were genotypically multidrug-resistant, consistently encoded seh, and intermittently (34/194) encoded an undisrupted hlb gene with concomitant absence of the lysogenic phage-encoded genes sak and scn. All MRSA also harboured a characteristic ~5350 nt insertion in SCCmec adjacent to orfX. Detailed demographic data from Denmark showed that there, the clone is typically (25/35) found in the community, and often (10/35) among individuals with links to South-Eastern Europe. This study elucidated the evolution and epidemiology of European CC1-MRSA-IV, which emerged from a meticillin-susceptible lineage prevalent in North-Eastern Romania before disseminating rapidly throughout Europe.