Opening the Museum's Vault: Historical Field Records Preserve Reliable Ecological Data.

AbstractMuseum specimens have long served as foundational data sources for ecological, evolutionary, and environmental research. Continued reimagining of museum collections is now also generating new types of data associated with but beyond physical specimens, a concept known as "extended specimens." Field notes penned by generations of naturalists contain firsthand ecological observations associated with museum collections and comprise a form of extended specimens with the potential to provide novel ecological data spanning broad geographic and temporal scales. Despite their data-yielding potential, however, field notes remain underutilized in research because of their heterogeneous, unstandardized, and qualitative nature. We introduce an approach for transforming descriptive ecological notes into quantitative data suitable for statistical analysis. Tests with simulated and real-world published data show that field notes and our transformation approach retain reliable quantitative ecological information under a range of sample sizes and evolutionary scenarios. Unlocking the wealth of data contained within field records could facilitate investigations into the ecology of clades whose diversity, distribution, or other demographic features present challenges to traditional ecological studies, improve our understanding of long-term environmental and evolutionary change, and enhance predictions of future change.

A One Health approach based on genomics for enhancing the Salmonella enterica surveillance in Colombia.

Objectives: This study aimed to provide evidence of the domestic benefits of introducing an integrative genomic analysis from the One Health approach in the national surveillance of Salmonella enterica between 1997-2017 in Colombia. Methods: Data on Salmonella from clinical laboratory-based surveillance between 1997-2017 and from a national cross-sectional study at chicken retail stores in Colombia were compared using a phenotypic, molecular, and genomic approaches. Additional analysis by serovar using single nucleotide polymorphism was developed to increase the resolution of the relatedness between the interfaces. Results: Locally, the diversity and pathogenic factors of the prevalent S. enterica serovars associated with foodborne disease in Colombia were described using laboratory, pulse field gel electrophoresis, and whole genome sequencing data. For example, the resolution of pulse field gel electrophoresis allowed the description of two main foodborne clusters of Salmonella Enteritidis isolates, which were expanded to eight foodborne clades using whole genome sequencing. Likewise, virulence factors and antimicrobial resistance determinants, and mobile genetic elements that converged in the foodborne clades should be considered a public health concern in Colombia. All results by serovar were compiled in an interactive easy to share report. Conclusion: Whole genome sequencing is a technology that provides a precise assessment of emerging foodborne risks such as the Salmonella foodborne clades, but it requires an integrative and continued collaboration between the stakeholders across the One Health sectors to promote appropriated actions and policies in public health.

The nature of science: The fundamental role of natural history in ecology, evolution, conservation, and education.

There is a contemporary trend in many major research institutions to de-emphasize the importance of natural history education in favor of theoretical, laboratory, or simulation-based research programs. This may take the form of removing biodiversity and field courses from the curriculum and the sometimes subtle maligning of natural history research as a "lesser" branch of science. Additional threats include massive funding cuts to natural history museums and the maintenance of their collections, the extirpation of taxonomists across disciplines, and a critical under-appreciation of the role that natural history data (and other forms of observational data, including Indigenous knowledge) play in the scientific process. In this paper, we demonstrate that natural history knowledge is integral to any competitive science program through a comprehensive review of the ways in which they continue to shape modern theory and the public perception of science. We do so by reviewing how natural history research has guided the disciplines of ecology, evolution, and conservation and how natural history data are crucial for effective education programs and public policy. We underscore these insights with contemporary case studies, including: how understanding the dynamics of evolutionary radiation relies on natural history data; methods for extracting novel data from museum specimens; insights provided by multi-decade natural history programs; and how natural history is the most logical venue for creating an informed and scientifically literate society. We conclude with recommendations aimed at students, university faculty, and administrators for integrating and supporting natural history in their mandates. Fundamentally, we are all interested in understanding the natural world, but we can often fall into the habit of abstracting our research away from its natural contexts and complexities. Doing so risks losing sight of entire vistas of new questions and insights in favor of an over-emphasis on simulated or overly controlled studies.

Prevalence and antimicrobial resistance of Escherichia coli and Salmonella spp. in animal feed in Colombia.

Objective: To determine the prevalence and antimicrobial resistance of Escherichia coli and Salmonella spp. in animal feed samples collected between 2018 and 2021 in Colombia. Methods: This was a laboratory-based cross-sectional study using routine data from the program for inspection, surveillance, and control of animal feed at the Colombian Agriculture Institute. Samples of animal feed for swine, poultry, canine, feline, leporine, piscine, and equine species were processed for detection of E. coli and Salmonella spp. using enrichment and selective culture methods. Isolates were tested for antimicrobial susceptibility using an automated microdilution method. Results: Of 1 748 animal feed samples analyzed, 83 (4.7%) were positive for E. coli and 66 (3.8%) for Salmonella spp. The presence of E. coli and Salmonella spp. was highest in feed for poultry (6.4% and 5.5%) and swine (6.1% and 4.3%). Antimicrobial resistance testing was performed in 27 (33%) E. coli isolates and 26 (39%) Salmonella isolates. Among E. coli, resistance was most frequently observed to ampicillin (44.5%) followed by cefazolin (33.3%), ciprofloxacin (29.6%), ampicillin/sulbactam (26%), and ceftriaxone (11.1%). The highest resistance levels in Salmonella spp. isolates were against cefazolin (7.7%) and piperacillin/tazobactam (7.7%). Conclusions: This is the first study from Colombia reporting on the prevalence and antimicrobial resistance of E. coli and Salmonella spp. in animal feed samples. Its results establish a baseline over a wide geographical distribution in Colombia. It highlights the need to integrate antimicrobial resistance surveillance in animal feed due to the emergence of resistant bacteria in this important stage of the supply chain.

Multidrug-resistant Salmonella spp. in fecal samples of pigs with suspected salmonellosis in Antioquia, Colombia, 2019-2021.

Objectives: To determine the proportion of Salmonella enterica in fecal samples of live pigs with suspected salmonellosis analyzed at the diagnostic unit of the University of Antioquia, Colombia between 2019 and 2021, and examine the serotypes and antimicrobial resistance patterns. Methods: This was a laboratory-based cross-sectional study of routine data on fecal samples received from pig farms in all nine subregions of Antioquia state, Colombia. Salmonella spp. detection at the university is done using enrichment, selective culture, and polymerase chain reaction. Serotypes were identified using the Kauffmann-White scheme and isolates were tested for antimicrobial susceptibility using broth microdilution. Results: Of 653 samples tested, 149 (23%) were positive for S. enterica. Nine serotypes were identified. The most common were Salmonella Typhimurium (56%) and its monophasic variant (35%). Resistance to ampicillin (70%) was most frequently observed, followed by ciprofloxacin (55%), and sulfamethoxazole-trimethoprim (52%). No isolates were resistant to amikacin and gentamicin. Multidrug resistance (resistance to ≥ 3 classes of antibiotics) was observed in 61 (44%) isolates. Multidrug resistance was highest in S. Typhimurium (57%) compared with the other serotypes. Serotype was associated with multidrug resistance (p = 0.01), but age of the pig and sub-region were not. Conclusions: The proportion of Salmonella spp. and the associated high levels of multidrug resistance are of concern and may indicate irrational use of antimicrobials and poor management practices in pig production systems in the region. Strengthened surveillance is needed to monitor and improve farm management practices and the use of antimicrobials in farms in Colombia.

Prevalence and antimicrobial resistance of Escherichia coli and Salmonella spp. in animal feed in Colombia

[ABSTRACT]. Objective. To determine the prevalence and antimicrobial resistance of Escherichia coli and Salmonella spp. in animal feed samples collected between 2018 and 2021 in Colombia. Methods. This was a laboratory-based cross-sectional study using routine data from the program for inspec- tion, surveillance, and control of animal feed at the Colombian Agriculture Institute. Samples of animal feed for swine, poultry, canine, feline, leporine, piscine, and equine species were processed for detection of E. coli and Salmonella spp. using enrichment and selective culture methods. Isolates were tested for antimicrobial susceptibility using an automated microdilution method. Results. Of 1 748 animal feed samples analyzed, 83 (4.7%) were positive for E. coli and 66 (3.8%) for Salmonella spp. The presence of E. coli and Salmonella spp. was highest in feed for poultry (6.4% and 5.5%) and swine (6.1% and 4.3%). Antimicrobial resistance testing was performed in 27 (33%) E. coli isolates and 26 (39%) Salmonella isolates. Among E. coli, resistance was most frequently observed to ampicillin (44.5%) followed by cefazolin (33.3%), ciprofloxacin (29.6%), ampicillin/sulbactam (26%), and ceftriaxone (11.1%). The highest resistance levels in Salmonella spp. isolates were against cefazolin (7.7%) and piperacillin/tazobactam (7.7%). Conclusions. This is the first study from Colombia reporting on the prevalence and antimicrobial resistance of E. coli and Salmonella spp. in animal feed samples. Its results establish a baseline over a wide geographical distribution in Colombia. It highlights the need to integrate antimicrobial resistance surveillance in animal feed due to the emergence of resistant bacteria in this important stage of the supply chain.

[RESUMEN]. Objetivo. Determinar la prevalencia y resistencia a los antimicrobianos de Escherichia coli y Salmonella spp. en muestras de piensos para animales tomadas entre el 2018 y el 2021 en Colombia. Métodos. Se trata de un estudio transversal realizado en el laboratorio a partir de los datos regulares del programa de inspección, vigilancia y control de alimentos para animales del Instituto Colombiano Agropec- uario. Se procesaron muestras de alimentos utilizados en la cría de cerdos, aves de corral, cánidos, félidos, lepóridos, peces y equinos con el fin de detectar E. coli y Salmonella spp. por medio de métodos de enriquec- imiento y cultivo selectivo. Se analizó la sensibilidad a los antimicrobianos de las cepas aisladas mediante microdilución automatizada. Resultados. De 1748 muestras de alimentos analizadas, 83 (4,7%) resultaron positivas para E. coli y 66 (3,8%) para Salmonella spp. La presencia de E. coli y Salmonella spp. fue mayor en los alimentos para aves de corral (6,4% y 5,5%) y cerdos (6,1% y 4,3%). Se realizaron pruebas de resistencia a los antimicrobianos en 27 (33%) cepas de E. coli y 26 (39%) de Salmonella. En las cepas de E. coli, se observó una mayor resis- tencia a la ampicilina (44,5%), seguida de la resistencia a la cefazolina (33,3%), la ciprofloxacina (29,6%), la ampicilina/sulbactam (26%) y la ceftriaxona (11,1%). En el caso de las cepas de Salmonella spp., los niveles de resistencia más elevados fueron para la cefazolina (7,7%) y piperacilina/tazobactam (7,7%). Conclusiones. Este es el primer estudio realizado en Colombia en el que se informa sobre la prevalencia y la resistencia a los antimicrobianos de E. coli y Salmonella spp. en muestras de alimentos para animales. Sus resultados establecen una línea de base para una zona geográfica mucho mayor dentro de Colombia. Se subraya la necesidad de integrar la vigilancia de la resistencia a los antimicrobianos en los alimentos para animales debido a la aparición de bacterias resistentes en esta importante etapa de la cadena de suministro.

[RESUMO]. Objetivo. Determinar a prevalência e a resistência a antimicrobianos de Escherichia coli e Salmonela spp. em amostras de ração animal coletadas entre 2018 e 2021 na Colômbia. Métodos. Estudo transversal de base laboratorial, usando dados de rotina do programa de inspeção, vig- ilância e controle de ração animal do Instituto Colombiano de Agricultura. Amostras de ração animal para as espécies suína, avícola, canina, felina, leporina, piscina e equina foram processadas para detecção de E. coli e Salmonella spp., usando métodos de enriquecimento e cultura seletiva. Os isolados foram testados quanto à suscetibilidade a antimicrobianos usando um método automatizado de microdiluição. Resultados. Das 1.748 amostras de ração animal analisadas, 83 (4,7%) foram positivas para E. coli e 66 (3,8%) para Salmonella spp. A presença de E. coli e Salmonella spp. foi maior em rações para aves (6,4% e 5,5%) e suínos (6,1% e 4,3%). O teste de resistência a antimicrobianos foi realizado em 27 (33%) isolados de E. coli e 26 (39%) isolados de Salmonella. Em E. coli, a resistência observada com maior frequência foi à ampicilina (44,5%), seguida da cefazolina (33,3%), ciprofloxacino (29,6%), ampicilina/sulbactam (26%) e ceftriaxona (11,1%). Os maiores níveis de resistência em isolados de Salmonella spp. foram contra cefazolina (7,7%) e piperacilina/tazobactam (7,7%). Conclusões. Este é o primeiro estudo da Colômbia a notificar a prevalência e resistência a antimicrobianos de E. coli e Salmonella spp. em amostras de ração animal. Os resultados estabelecem uma linha de base com ampla distribuição geográfica na Colômbia. Destaca-se a necessidade de integrar a vigilância da resistência a antimicrobianos na ração animal, devido ao surgimento de bactérias resistentes nesta importante etapa da cadeia de abastecimento.

Multidrug-resistant Salmonella spp. in fecal samples of pigs with suspected salmonellosis in Antioquia, Colombia, 2019–2021

[ABSTRACT]. Objectives. To determine the proportion of Salmonella enterica in fecal samples of live pigs with suspected salmonellosis analyzed at the diagnostic unit of the University of Antioquia, Colombia between 2019 and 2021, and examine the serotypes and antimicrobial resistance patterns. Methods. This was a laboratory-based cross-sectional study of routine data on fecal samples received from pig farms in all nine subregions of Antioquia state, Colombia. Salmonella spp. detection at the university is done using enrichment, selective culture, and polymerase chain reaction. Serotypes were identified using the Kauffmann–White scheme and isolates were tested for antimicrobial susceptibility using broth microdilution. Results. Of 653 samples tested, 149 (23%) were positive for S. enterica. Nine serotypes were identified. The most common were Salmonella Typhimurium (56%) and its monophasic variant (35%). Resistance to ampicillin (70%) was most frequently observed, followed by ciprofloxacin (55%), and sulfamethoxazole–trimethoprim (52%). No isolates were resistant to amikacin and gentamicin. Multidrug resistance (resistance to ≥ 3 classes of antibiotics) was observed in 61 (44%) isolates. Multidrug resistance was highest in S. Typhimurium (57%) compared with the other serotypes. Serotype was associated with multidrug resistance (p = 0.01), but age of the pig and sub-region were not. Conclusions. The proportion of Salmonella spp. and the associated high levels of multidrug resistance are of concern and may indicate irrational use of antimicrobials and poor management practices in pig production systems in the region. Strengthened surveillance is needed to monitor and improve farm management prac- tices and the use of antimicrobials in farms in Colombia.

[RESUMEN]. Objetivos. Determinar la proporción de Salmonella enterica en muestras fecales de cerdos vivos con pre- sunta salmonelosis analizadas en la unidad de diagnóstico de la Universidad de Antioquia (Colombia) entre el 2019 y el 2021, así como examinar los serotipos y los patrones de resistencia a los antimicrobianos. Métodos. Se trata de un estudio transversal de laboratorio sobre datos ordinarios de muestras fecales pro- venientes de granjas porcinas de las nueve subregiones del departamento de Antioquia (Colombia). La detección de Salmonella spp. en la universidad se realiza mediante el enriquecimiento, el cultivo selectivo y la reacción en cadena de la polimerasa. Se identificaron los serotipos con el esquema de Kauffmann-White y se examinaron las cepas aisladas para determinar la susceptibilidad antimicrobiana mediante microdilución en caldo. Resultados. De las 653 muestras analizadas, 149 (23%) dieron un resultado positivo para S. enterica. Se iden- tificaron nueve serotipos. Los más comunes fueron Salmonella typhimurium (56%) y su variante monofásica (35%). La resistencia a la ampicilina fue la observada con mayor frecuencia (70%), seguida de la resisten- cia al ciprofloxacino (55%) y al sulfametoxazol-trimetoprima (52%). Ninguna cepa aislada fue resistente a la amikacina y la gentamicina. Se observó resistencia a múltiples fármacos (resistencia a tres o más clases de antibióticos) en 61 cepas (44%). La resistencia a múltiples fármacos fue más elevada en el caso de S. typh- imurium (57%) en comparación con los otros serotipos. Se asoció el serotipo con la resistencia a múltiples fármacos (p = 0,01), a diferencia de la edad del cerdo y la subregión. Conclusiones. La proporción de Salmonella spp. y los elevados niveles asociados de resistencia a múltiples fármacos son preocupantes y pueden ser un indicativo de uso irracional de antimicrobianos y malas prácticas de gestión en los sistemas de producción porcina de la región. Es necesario reforzar la vigilancia para dar seguimiento y mejorar las prácticas de gestión agropecuaria y el uso de antimicrobianos en las granjas en Colombia.

[RESUMO]. Objetivos. Determinar a proporção de Salmonella enterica em amostras de fezes de suínos vivos com sus- peita de salmonelose analisadas na unidade de diagnóstico da Universidade de Antioquia, Colômbia, entre 2019 e 2021, e examinar seus sorotipos e padrões de resistência a antimicrobianos. Métodos. Estudo transversal, de base laboratorial, utilizando dados de rotina de amostras de fezes recebidas de suinocultores em todas as nove sub-regiões do estado de Antioquia, Colômbia. A detecção de Salmonella spp. na Universidade é feita por enriquecimento, cultura seletiva e reação em cadeia da polimerase. Os sorotipos foram identificados usando o esquema de Kauffmann-White, e os isolados foram testados quanto à suscetibilidade aos antimicrobianos pelo método de microdiluição em caldo. Resultados. Das 653 amostras testadas, 149 (23%) foram positivas para S. enterica. Foram identificados nove sorotipos. Os mais comuns foram Salmonella Typhimurium (56%) e sua variante monofásica (35%). A resistência à ampicilina (70%) foi observada com maior frequência, seguida pela resistência ao ciprofloxa- cino (55%) e ao sulfametoxazol/trimetoprima (52%). Nenhum isolado apresentou resistência à amicacina ou gentamicina. Multirresistência (resistência a ≥ 3 classes de antibióticos) foi observada em 61 isolados (44%). A multirresistência foi mais comum em S. Typhimurium (57%), em comparação aos outros sorotipos. Foi con- statada associação da multirresistência com sorotipos (p = 0,01), mas não com idade do suíno ou sub-região. Conclusões. A proporção de Salmonella spp. e os níveis elevados associados de multirresistência a antimi- crobianos aqui constatados são preocupantes, e podem indicar uso irracional de antimicrobianos e práticas inadequadas de manejo nos sistemas de suinocultura da região. É preciso fortalecer a vigilância para moni- torar e melhorar as práticas de manejo agrícola e o uso de antimicrobianos em fazendas na Colômbia.

Exon-based Phylogenomics and the Relationships of African Cichlid Fishes: Tackling the Challenges of Reconstructing Phylogenies with Repeated Rapid Radiations.

African cichlids (subfamily: Pseudocrenilabrinae) are among the most diverse vertebrates, and their propensity for repeated rapid radiation has made them a celebrated model system in evolutionary research. Nonetheless, despite numerous studies, phylogenetic uncertainty persists, and riverine lineages remain comparatively underrepresented in higher-level phylogenetic studies. Heterogeneous gene histories resulting from incomplete lineage sorting (ILS) and hybridization are likely sources of uncertainty, especially during episodes of rapid speciation. We investigate the relationships of Pseudocrenilabrinae and its close relatives while accounting for multiple sources of genetic discordance using species tree and hybrid network analyses with hundreds of single-copy exons. We improve sequence recovery for distant relatives, thereby extending the taxonomic reach of our probes, with a hybrid reference guided/de novo assembly approach. Our analyses provide robust hypotheses for most higher-level relationships and reveal widespread gene heterogeneity, including in riverine taxa. ILS and past hybridization are identified as the sources of genetic discordance in different lineages. Sampling of various Blenniiformes (formerly Ovalentaria) adds strong phylogenomic support for convict blennies (Pholidichthyidae) as sister to Cichlidae and points to other potentially useful protein-coding markers across the order. A reliable phylogeny with representatives from diverse environments will support ongoing taxonomic and comparative evolutionary research in the cichlid model system. [African cichlids; Blenniiformes; Gene tree heterogeneity; Hybrid assembly; Phylogenetic network; Pseudocrenilabrinae; Species tree.].

Prevalence and antimicrobial resistance of Escherichia coli and Salmonella spp. in animal feed in Colombia / Prevalencia y resistencia a los antimicrobianos de Escherichia coli y Salmonella spp. en los alimentos para animales en Colombia / Prevalência e resistência a antimicrobianos de Escherichia coli e Salmonella spp. em ração animal na Colômbia

ABSTRACT Objective. To determine the prevalence and antimicrobial resistance of Escherichia coli and Salmonella spp. in animal feed samples collected between 2018 and 2021 in Colombia. Methods. This was a laboratory-based cross-sectional study using routine data from the program for inspection, surveillance, and control of animal feed at the Colombian Agriculture Institute. Samples of animal feed for swine, poultry, canine, feline, leporine, piscine, and equine species were processed for detection of E. coli and Salmonella spp. using enrichment and selective culture methods. Isolates were tested for antimicrobial susceptibility using an automated microdilution method. Results. Of 1 748 animal feed samples analyzed, 83 (4.7%) were positive for E. coli and 66 (3.8%) for Salmonella spp. The presence of E. coli and Salmonella spp. was highest in feed for poultry (6.4% and 5.5%) and swine (6.1% and 4.3%). Antimicrobial resistance testing was performed in 27 (33%) E. coli isolates and 26 (39%) Salmonella isolates. Among E. coli, resistance was most frequently observed to ampicillin (44.5%) followed by cefazolin (33.3%), ciprofloxacin (29.6%), ampicillin/sulbactam (26%), and ceftriaxone (11.1%). The highest resistance levels in Salmonella spp. isolates were against cefazolin (7.7%) and piperacillin/tazobactam (7.7%). Conclusions. This is the first study from Colombia reporting on the prevalence and antimicrobial resistance of E. coli and Salmonella spp. in animal feed samples. Its results establish a baseline over a wide geographical distribution in Colombia. It highlights the need to integrate antimicrobial resistance surveillance in animal feed due to the emergence of resistant bacteria in this important stage of the supply chain.

RESUMEN Objetivo. Determinar la prevalencia y resistencia a los antimicrobianos de Escherichia coli y Salmonella spp. en muestras de piensos para animales tomadas entre el 2018 y el 2021 en Colombia. Métodos. Se trata de un estudio transversal realizado en el laboratorio a partir de los datos regulares del programa de inspección, vigilancia y control de alimentos para animales del Instituto Colombiano Agropecuario. Se procesaron muestras de alimentos utilizados en la cría de cerdos, aves de corral, cánidos, félidos, lepóridos, peces y equinos con el fin de detectar E. coli y Salmonella spp. por medio de métodos de enriquecimiento y cultivo selectivo. Se analizó la sensibilidad a los antimicrobianos de las cepas aisladas mediante microdilución automatizada. Resultados. De 1748 muestras de alimentos analizadas, 83 (4,7%) resultaron positivas para E. coli y 66 (3,8%) para Salmonella spp. La presencia de E. coli y Salmonella spp. fue mayor en los alimentos para aves de corral (6,4% y 5,5%) y cerdos (6,1% y 4,3%). Se realizaron pruebas de resistencia a los antimicrobianos en 27 (33%) cepas de E. coli y 26 (39%) de Salmonella. En las cepas de E. coli, se observó una mayor resistencia a la ampicilina (44,5%), seguida de la resistencia a la cefazolina (33,3%), la ciprofloxacina (29,6%), la ampicilina/sulbactam (26%) y la ceftriaxona (11,1%). En el caso de las cepas de Salmonella spp., los niveles de resistencia más elevados fueron para la cefazolina (7,7%) y piperacilina/tazobactam (7,7%). Conclusiones. Este es el primer estudio realizado en Colombia en el que se informa sobre la prevalencia y la resistencia a los antimicrobianos de E. coli y Salmonella spp. en muestras de alimentos para animales. Sus resultados establecen una línea de base para una zona geográfica mucho mayor dentro de Colombia. Se subraya la necesidad de integrar la vigilancia de la resistencia a los antimicrobianos en los alimentos para animales debido a la aparición de bacterias resistentes en esta importante etapa de la cadena de suministro.

RESUMO Objetivo. Determinar a prevalência e a resistência a antimicrobianos de Escherichia coli e Salmonela spp. em amostras de ração animal coletadas entre 2018 e 2021 na Colômbia. Métodos. Estudo transversal de base laboratorial, usando dados de rotina do programa de inspeção, vigilância e controle de ração animal do Instituto Colombiano de Agricultura. Amostras de ração animal para as espécies suína, avícola, canina, felina, leporina, piscina e equina foram processadas para detecção de E. coli e Salmonella spp., usando métodos de enriquecimento e cultura seletiva. Os isolados foram testados quanto à suscetibilidade a antimicrobianos usando um método automatizado de microdiluição. Resultados. Das 1.748 amostras de ração animal analisadas, 83 (4,7%) foram positivas para E. coli e 66 (3,8%) para Salmonella spp. A presença de E. coli e Salmonella spp. foi maior em rações para aves (6,4% e 5,5%) e suínos (6,1% e 4,3%). O teste de resistência a antimicrobianos foi realizado em 27 (33%) isolados de E. coli e 26 (39%) isolados de Salmonella. Em E. coli, a resistência observada com maior frequência foi à ampicilina (44,5%), seguida da cefazolina (33,3%), ciprofloxacino (29,6%), ampicilina/sulbactam (26%) e ceftriaxona (11,1%). Os maiores níveis de resistência em isolados de Salmonella spp. foram contra cefazolina (7,7%) e piperacilina/tazobactam (7,7%). Conclusões. Este é o primeiro estudo da Colômbia a notificar a prevalência e resistência a antimicrobianos de E. coli e Salmonella spp. em amostras de ração animal. Os resultados estabelecem uma linha de base com ampla distribuição geográfica na Colômbia. Destaca-se a necessidade de integrar a vigilância da resistência a antimicrobianos na ração animal, devido ao surgimento de bactérias resistentes nesta importante etapa da cadeia de abastecimento.

Multidrug-resistant Salmonella spp. in fecal samples of pigs with suspected salmonellosis in Antioquia, Colombia, 2019-2021 / Salmonella spp. multirresistentes en muestras fecales de cerdos con presunta salmonelosis en Antioquia, Colombia, 2019-2021 / Salmonella spp. multirresistente em amostras fecais de suínos com suspeita de salmonelose em Antioquia, Colômbia, 2019-2021

ABSTRACT Objectives. To determine the proportion of Salmonella enterica in fecal samples of live pigs with suspected salmonellosis analyzed at the diagnostic unit of the University of Antioquia, Colombia between 2019 and 2021, and examine the serotypes and antimicrobial resistance patterns. Methods. This was a laboratory-based cross-sectional study of routine data on fecal samples received from pig farms in all nine subregions of Antioquia state, Colombia. Salmonella spp. detection at the university is done using enrichment, selective culture, and polymerase chain reaction. Serotypes were identified using the Kauffmann-White scheme and isolates were tested for antimicrobial susceptibility using broth microdilution. Results. Of 653 samples tested, 149 (23%) were positive for S. enterica. Nine serotypes were identified. The most common were Salmonella Typhimurium (56%) and its monophasic variant (35%). Resistance to ampicillin (70%) was most frequently observed, followed by ciprofloxacin (55%), and sulfamethoxazole-trimethoprim (52%). No isolates were resistant to amikacin and gentamicin. Multidrug resistance (resistance to ≥ 3 classes of antibiotics) was observed in 61 (44%) isolates. Multidrug resistance was highest in S. Typhimurium (57%) compared with the other serotypes. Serotype was associated with multidrug resistance (p = 0.01), but age of the pig and sub-region were not. Conclusions. The proportion of Salmonella spp. and the associated high levels of multidrug resistance are of concern and may indicate irrational use of antimicrobials and poor management practices in pig production systems in the region. Strengthened surveillance is needed to monitor and improve farm management practices and the use of antimicrobials in farms in Colombia.

RESUMEN Objetivos. Determinar la proporción de Salmonella enterica en muestras fecales de cerdos vivos con presunta salmonelosis analizadas en la unidad de diagnóstico de la Universidad de Antioquia (Colombia) entre el 2019 y el 2021, así como examinar los serotipos y los patrones de resistencia a los antimicrobianos. Métodos. Se trata de un estudio transversal de laboratorio sobre datos ordinarios de muestras fecales provenientes de granjas porcinas de las nueve subregiones del departamento de Antioquia (Colombia). La detección de Salmonella spp. en la universidad se realiza mediante el enriquecimiento, el cultivo selectivo y la reacción en cadena de la polimerasa. Se identificaron los serotipos con el esquema de Kauffmann-White y se examinaron las cepas aisladas para determinar la susceptibilidad antimicrobiana mediante microdilución en caldo. Resultados. De las 653 muestras analizadas, 149 (23%) dieron un resultado positivo para S. enterica. Se identificaron nueve serotipos. Los más comunes fueron Salmonella typhimurium (56%) y su variante monofásica (35%). La resistencia a la ampicilina fue la observada con mayor frecuencia (70%), seguida de la resistencia al ciprofloxacino (55%) y al sulfametoxazol-trimetoprima (52%). Ninguna cepa aislada fue resistente a la amikacina y la gentamicina. Se observó resistencia a múltiples fármacos (resistencia a tres o más clases de antibióticos) en 61 cepas (44%). La resistencia a múltiples fármacos fue más elevada en el caso de S. typhimurium (57%) en comparación con los otros serotipos. Se asoció el serotipo con la resistencia a múltiples fármacos (p = 0,01), a diferencia de la edad del cerdo y la subregión. Conclusiones. La proporción de Salmonella spp. y los elevados niveles asociados de resistencia a múltiples fármacos son preocupantes y pueden ser un indicativo de uso irracional de antimicrobianos y malas prácticas de gestión en los sistemas de producción porcina de la región. Es necesario reforzar la vigilancia para dar seguimiento y mejorar las prácticas de gestión agropecuaria y el uso de antimicrobianos en las granjas en Colombia.

RESUMO Objetivos. Determinar a proporção de Salmonella enterica em amostras de fezes de suínos vivos com suspeita de salmonelose analisadas na unidade de diagnóstico da Universidade de Antioquia, Colômbia, entre 2019 e 2021, e examinar seus sorotipos e padrões de resistência a antimicrobianos. Métodos. Estudo transversal, de base laboratorial, utilizando dados de rotina de amostras de fezes recebidas de suinocultores em todas as nove sub-regiões do estado de Antioquia, Colômbia. A detecção de Salmonella spp. na Universidade é feita por enriquecimento, cultura seletiva e reação em cadeia da polimerase. Os sorotipos foram identificados usando o esquema de Kauffmann-White, e os isolados foram testados quanto à suscetibilidade aos antimicrobianos pelo método de microdiluição em caldo. Resultados. Das 653 amostras testadas, 149 (23%) foram positivas para S. enterica. Foram identificados nove sorotipos. Os mais comuns foram Salmonella Typhimurium (56%) e sua variante monofásica (35%). A resistência à ampicilina (70%) foi observada com maior frequência, seguida pela resistência ao ciprofloxacino (55%) e ao sulfametoxazol/trimetoprima (52%). Nenhum isolado apresentou resistência à amicacina ou gentamicina. Multirresistência (resistência a ≥ 3 classes de antibióticos) foi observada em 61 isolados (44%). A multirresistência foi mais comum em S. Typhimurium (57%), em comparação aos outros sorotipos. Foi constatada associação da multirresistência com sorotipos (p = 0,01), mas não com idade do suíno ou sub-região. Conclusões. A proporção de Salmonella spp. e os níveis elevados associados de multirresistência a antimicrobianos aqui constatados são preocupantes, e podem indicar uso irracional de antimicrobianos e práticas inadequadas de manejo nos sistemas de suinocultura da região. É preciso fortalecer a vigilância para monitorar e melhorar as práticas de manejo agrícola e o uso de antimicrobianos em fazendas na Colômbia.

Development of a Phage Cocktail to Target Salmonella Strains Associated with Swine.

Infections caused by multidrug resistant Salmonella strains are problematic in swine and are entering human food chains. Bacteriophages (phages) could be used to complement or replace antibiotics to reduce infection within swine. Here, we extensively characterised six broad host range lytic Salmonella phages, with the aim of developing a phage cocktail to prevent or treat infection. Intriguingly, the phages tested differed by one to five single nucleotide polymorphisms. However, there were clear phenotypic differences between them, especially in their heat and pH sensitivity. In vitro killing assays were conducted to determine the efficacy of phages alone and when combined, and three cocktails reduced bacterial numbers by ~2 × 103 CFU/mL within two hours. These cocktails were tested in larvae challenge studies, and prophylactic treatment with phage cocktail SPFM10-SPFM14 was the most efficient. Phage treatment improved larvae survival to 90% after 72 h versus 3% in the infected untreated group. In 65% of the phage-treated larvae, Salmonella counts were below the detection limit, whereas it was isolated from 100% of the infected, untreated larvae group. This study demonstrates that phages effectively reduce Salmonella colonisation in larvae, which supports their ability to similarly protect swine.

The gut microbiota of chickens in a commercial farm treated with a Salmonella phage cocktail.

The microbiota in broiler chicken intestines affects the animals' health, metabolism, and immunity both positively and negatively. Accordingly, it has a significant impact on animal productivity. Phages, host-specific parasites of bacterial cells, are a promising antimicrobial alternative that selectively target pathogens without disturbing the microbiota. The purpose of this study is to further characterize the commensal microbial community at production scale in broiler chickens treated with a Salmonella phage treatment. We evaluated the cecal microbiota of broilers reared in a commercial farming system where a phage cocktail against Salmonella, SalmoFree was supplied to animals. To do so, two field trials were conducted, incorporating three doses of phages in the broilers' drinking water. Our results showed that the core microbiome (taxa that were present in more than 50% of samples) contained species that are key to microbiota adaptation in the last stage of the production cycle. Among these, there are some important degraders of complex polysaccharides and producers of short chain fatty acids (SCFA) such as Eisenbergiella and Lachnoclostridium. The phage cocktail did not affect the normal development of the microbiota's structure. The addition of the phage cocktail resulted in a significant reduction in Campylobacter and an increase in Butyricimonas, Helicobacter and Rikenellaceae, which are common inhabitants in chicken gut with known negative and positive effects on their health and metabolism. Altogether, we consider that these results contribute valuable information to the implementation of large-scale phage therapy technologies.

Bacterial meta-analysis of chicken cecal microbiota.

Poultry production is an industry that generates 90,000 metric tons of chicken meat worldwide. Thus, optimizing chicken growth and sustainable production is of great importance. A central factor determining not only production parameters, but also stability of the immune system and chicken health, is the diversity and variability of the microbiota present throughout the gastrointestinal tract. To date, several studies have investigated the relationship between bacterial communities and the gut microbiome, with limited data to compare. This study aims to create a bacterial meta-analysis based on studies using amplicon sequencing with Illumina sequencing technologies in order to build a baseline for comparison in future analyses of the cecal bacterial composition in chicken. A systematic literature review was performed (SYRF ID: e84f0468-e418-4eec-9da4-b517f1b4809d. Full project URL: https://app.syrf.org.uk/projects/e84f0468-e418-4eec-9da4-b517f1b4809d/detail). From all the available and analyzed manuscripts only nine contained full raw-sequence data available and the corresponding metadata. A total of 324 samples, comprising three different regions within the 16S rRNA gene, were analyzed. Due to the heterogeneity of the data, each region was analyzed independently and an effort for a joint analysis was performed as well. Taxonomic profiling revealed 11 phyla, with Firmicutes as the most prevalent phylum, followed by Bacteroidetes and Proteobacteria. At genus level, 109 genera were found. Shannon metric for alpha diversity showed that factors like type of chickens (Commercial or experimental) and 16S rRNA gene subregion have negligible effect on diversity. Despite the large number of parameters that were taken into account, the identification of common bacteria showed five genera to be common for all sets in at least 50% of the samples. These genera are highly associated to cellulose degradation and short chain fatty acids synthesis. In general, it was possible to identify some commonalities in the bacterial cecal microbial community despite the extensive variability and factors differing from one study to another.

Economic evaluation of the development of a phage therapy product for the control of Salmonella in poultry.

Poultry products are one of the major transmission media of Salmonella enteritidis to humans. A promising alternative to reduce the load of Salmonella in poultry are bacteriophages. Elsewhere, a mixture of six bacteriophages has been used successfully, but large-scale production would be necessary to supply potential poultry market and costs analyses have not been calculated yet. For this, a powerful tool to predict production costs is bioprocess modeling coupled with economic analyses. This work aims to model the scaled-up production of a six bacteriophages mixture based on a laboratory/pilot-scale production using Biosolve Process. For the model construction, a combination of experimental and reported data was applied, in which different production alternatives and the range of 1-100% of the Colombian poultry market (at broiler's farm and slaughterhouse) were analyzed. Results indicate that the best cost-effective process configuration/scale is to use one bioreactor (156 L) for the six bacteriophages, then a 0.45 µm filtration for removal of biomass, and a 0.22 µm filtration for sterility; this to supply the 35% of the market size for broiler farms (equivalent to 210 million chickens). This configuration gives a production cost per chicken of US$ 0.02. Additionally, a sensitivity analysis and a theoretical contrast for understanding the impact that titer and recovery have on production scale determined that titer affects the most the cost and requires optimization. The present works serves as a first, and required, approach for the development of phage therapy products that are alternatives to present-day pathogens control strategies.

Host Resistance, Genomics and Population Dynamics in a Salmonella Enteritidis and Phage System.

Bacteriophages represent an alternative solution to control bacterial infections. When interacting, bacteria and phage can evolve, and this relationship is described as antagonistic coevolution, a pattern that does not fit all models. In this work, the model consisted of a microcosm of Salmonella enterica serovar Enteritidis and φSan23 phage. Samples were taken for 12 days every 48 h. Bacteria and phage samples were collected; and isolated bacteria from each time point were challenged against phages from previous, contemporary, and subsequent time points. The phage plaque tests, with the genomics analyses, showed a mutational asymmetry dynamic in favor of the bacteria instead of antagonistic coevolution. This is important for future phage-therapy applications, so we decided to explore the population dynamics of Salmonella under different conditions: pressure of one phage, a combination of phages, and phages plus an antibiotic. The data from cultures with single and multiple phages, and antibiotics, were used to create a mathematical model exploring population and resistance dynamics of Salmonella under these treatments, suggesting a nonlethal, growth-inhibiting antibiotic may decrease resistance to phage-therapy cocktails. These data provide a deep insight into bacterial dynamics under different conditions and serve as additional criteria to select phages and antibiotics for phage-therapy.

Genomic Characterization of Extended-Spectrum Cephalosporin-Resistant Salmonella enterica in the Colombian Poultry Chain.

Salmonella enterica serovars have been isolated from Colombian broilers and broiler meat. The aim of this study was to investigate the diversity of ESBL/pAmpC genes in extended-spectrum cephalosporin resistant Salmonella enterica and the phylogeny of ESBL/pAmpC-carrying Salmonella using Whole Genome Sequencing (WGS). A total of 260 cefotaxime resistant Salmonella isolates, obtained between 2008 and 2013 from broiler farms, slaughterhouses and retail, were included. Isolates were screened by PCR for ESBL/pAmpC genes. Gene and plasmid subtyping and strain Multi Locus Sequence Typing was performed in silico for a selection of fully sequenced isolates. Core-genome-based analyses were performed per ST encountered. bla CMY-2-like was carried in 168 isolates, 52 carried bla CTX-M-2 group, 7 bla SHV, 5 a combination of bla CMY-2-like-bla SHV and 3 a combination of bla CMY-2-like-bla CTX-M-2 group. In 25 isolates no ESBL/pAmpC genes that were screened for were found. WGS characterization of 36 selected strains showed plasmid-encoded bla CMY-2 in 21, bla CTX-M-165 in 11 and bla SHV-12 in 7 strains. These genes were mostly carried on IncI1/ST12, IncQ1, and IncI1/ST231 plasmids, respectively. Finally, 17 strains belonged to S. Heidelberg ST15, 16 to S. Paratyphi B variant Java ST28, 1 to S. Enteritidis ST11, 1 to S. Kentucky ST152 and 1 to S. Albany ST292. Phylogenetic comparisons with publicly available genomes showed separate clustering of Colombian S. Heidelberg and S. Paratyphi B var. Java. In conclusion, resistance to extended-spectrum cephalosporins in Salmonella from Colombian poultry is mainly encoded by bla CMY-2 and bla CTX-M-165 genes. These genes are mostly associated with IncI1/ST12 and IncQ1 plasmids, respectively. Evolutionary divergence is observed between Colombian S. Heidelberg and S. Paratyphi B var. Java and those from other countries.

The gastrointestinal microbiome and its association with the control of pathogens in broiler chicken production: A review.

The microbiome of the broiler chicken gastrointestinal tract (GIT) has been extensively studied, and it has been amply demonstrated that it plays an important role in the health of the host, as it has a positive impact on the immune system, the physiology of the GIT, and productivity. Also, the microbiota is involved in reducing and preventing colonization by enteric pathogens through the process of competitive exclusion and the production of bacteriostatic and bactericidal substances. The taxonomic composition of the microbiota is affected by different factors, such as the organ, the age of the animal, diet and the use of antimicrobials.Different kinds of additives that regulate the microbial community in feed include probiotics (live microorganisms that when administered in adequate amounts confer a health benefit on the host), prebiotics (ingredients that stimulate increased beneficial microbial activity in the digestive system in order to improve the health of the host) and phytobiotics (primary or secondary components of plants that contain bioactive compounds that exert a positive effect on the growth and health of animals). Phages may potentially provide an integrated solution to modulate the intestinal microbiome of chicken intestines, as they reduce specific pathogenic microbial populations, permitting the proliferation of beneficial microbiota. Studies have shown that the use of cocktails of phages, especially in high concentrations and with short lapses of time between exposure to the bacteria and treatment with phages, optimize the reduction of Salmonella in chickens. Each of these technologies has demonstrable positive effects on the health of the host and the reduction of the pathogen load in controlled assays.This paper presents a comprehensive summary of the role of the microbiota in the broiler chicken gastrointestinal tract, and discusses the usefulness of different strategies for its modulation to control pathogens, with a particular emphasis on bacteriophages.

High Heterogeneity of Escherichia coli Sequence Types Harbouring ESBL/AmpC Genes on IncI1 Plasmids in the Colombian Poultry Chain.

BACKGROUND: Escherichia coli producing ESBL/AmpC enzymes are unwanted in animal production chains as they may pose a risk to human and animal health. Molecular characterization of plasmids and strains carrying genes that encode these enzymes is essential to understand their local and global spread. OBJECTIVES: To investigate the diversity of genes, plasmids and strains in ESBL/AmpC-producing E. coli from the Colombian poultry chain isolated within the Colombian Integrated Program for Antimicrobial Resistance Surveillance (Coipars). METHODS: A total of 541 non-clinical E. coli strains from epidemiologically independent samples and randomly isolated between 2008 and 2013 within the Coipars program were tested for antimicrobial susceptibility. Poultry isolates resistant to cefotaxime (MIC ≥ 4 mg/L) were screened for ESBL/AmpC genes including blaCTX-M, blaSHV, blaTEM, blaCMY and blaOXA. Plasmid and strain characterization was performed for a selection of the ESBL/AmpC-producing isolates. Plasmids were purified and transformed into E. coli DH10B cells or transferred by conjugation to E. coli W3110. When applicable, PCR Based Replicon Typing (PBRT), plasmid Multi Locus Sequence Typing (pMLST), plasmid Double Locus Sequence Typing (pDLST) and/or plasmid Replicon Sequence Typing (pRST) was performed on resulting transformants and conjugants. Multi Locus Sequence Typing (MLST) was used for strain characterization. RESULTS: In total, 132 of 541 isolates were resistant to cefotaxime and 122 were found to carry ESBL/AmpC genes. Ninety-two harboured blaCMY-2 (75%), fourteen blaSHV-12 (11%), three blaSHV-5 (2%), five blaCTX-M-2 (4%), one blaCTX-M-15 (1%), one blaCTX-M-8 (1%), four a combination of blaCMY-2 and blaSHV-12 (4%) and two a combination of blaCMY-2 and blaSHV-5 (2%). A selection of 39 ESBL/AmpC-producing isolates was characterized at the plasmid and strain level. ESBL/AmpC genes from 36 isolates were transferable by transformation or conjugation of which 22 were located on IncI1 plasmids. These IncI1 plasmids harboured predominantly blaCMY-2 (16/22), and to a lesser extend blaSHV-12 (5/22) and blaCTX-M-8 (1/22). Other plasmid families associated with ESBL/AmpC-genes were IncK (4/33), IncHI2 (3/33), IncA/C (2/33), IncΒ/O (1/33) and a non-typeable replicon (1/33). Subtyping of IncI1 and IncHI2 demonstrated IncI1/ST12 was predominantly associated with blaCMY-2 (12/16) and IncHI2/ST7 with blaCTX-M-2 (2/3). Finally, 31 different STs were detected among the 39 selected isolates. CONCLUSIONS: Resistance to extended spectrum cephalosporins in E. coli from Colombian poultry is mainly caused by blaCMY-2 and blaSHV-12. The high diversity of strain Sequence Types and the dissemination of homogeneous IncI1/ST12 plasmids suggest that spread of the resistance is mainly mediated by horizontal gene transfer.

Phage ΦPan70, a Putative Temperate Phage, Controls Pseudomonas aeruginosa in Planktonic, Biofilm and Burn Mouse Model Assays.

Pseudomonas aeruginosa is one of the Multi-Drug-Resistant organisms most frequently isolated worldwide and, because of a shortage of new antibiotics, bacteriophages are considered an alternative for its treatment. Previously, P. aeruginosa phages were isolated and best candidates were chosen based on their ability to form clear plaques and their host range. This work aimed to characterize one of those phages, ΦPan70, preliminarily identified as a good candidate for phage-therapy. We performed infection curves, biofilm removal assays, transmission-electron-microscopy, pulsed-field-gel-electrophoresis, and studied the in vivo ΦPan70 biological activity in the burned mouse model. ΦPan70 was classified as a member of the Myoviridae family and, in both planktonic cells and biofilms, was responsible for a significant reduction in the bacterial population. The burned mouse model showed an animal survival between 80% and 100%, significantly different from the control animals (0%). However, analysis of the ΦPan70 genome revealed that it was 64% identical to F10, a temperate P. aeruginosa phage. Gene annotation indicated ΦPan70 as a new, but possible temperate phage, therefore not ideal for phage-therapy. Based on this, we recommend genome sequence analysis as an early step to select candidate phages for potential application in phage-therapy, before entering into a more intensive characterization.

Selection towards different adaptive optima drove the early diversification of locomotor phenotypes in the radiation of Neotropical geophagine cichlids.

BACKGROUND: Simpson envisaged a conceptual model of adaptive radiation in which lineages diversify into "adaptive zones" within a macroevolutionary adaptive landscape. However, only a handful of studies have empirically investigated this adaptive landscape and its consequences for our interpretation of the underlying mechanisms of phenotypic evolution. In fish radiations the evolution of locomotor phenotypes may represent an important dimension of ecomorphological diversification given the implications of locomotion for feeding and habitat use. Neotropical geophagine cichlids represent a newly identified adaptive radiation and provide a useful system for studying patterns of locomotor diversification and the implications of selective constraints on phenotypic divergence in general. RESULTS: We use multivariate ordination, models of phenotypic evolution and posterior predictive approaches to investigate the macroevolutionary adaptive landscape and test for evidence of early divergence of locomotor phenotypes in Geophagini. The evolution of locomotor phenotypes was characterized by selection towards at least two distinct adaptive peaks and the early divergence of modern morphological disparity. One adaptive peak included the benthic and epibenthic invertivores and was characterized by fishes with deep, laterally compressed bodies that optimize precise, slow-swimming manoeuvres. The second adaptive peak resulted from a shift in adaptive optima in the species-rich ram-feeding/rheophilic Crenicichla-Teleocichla clade and was characterized by species with streamlined bodies that optimize fast starts and rapid manoeuvres. Evolutionary models and posterior predictive approaches favoured an early shift to a new adaptive peak over decreasing rates of evolution as the underlying process driving the early divergence of locomotor phenotypes. CONCLUSIONS: The influence of multiple adaptive peaks on the divergence of locomotor phenotypes in Geophagini is compatible with the expectations of an ecologically driven adaptive radiation. This study confirms that the diversification of locomotor phenotypes represents an important dimension of phenotypic evolution in the geophagine adaptive radiation. It also suggests that the commonly observed early burst of phenotypic evolution during adaptive radiations may be better explained by the concentration of shifts to new adaptive peaks deep in the phylogeny rather than overall decreasing rates of evolution.