Prevencíon de la matitis bovina : limitantes de manejo en lecherías especializadas.

Mundialmente se considera que la mastitis bovina es una de las enfermedades más costosa que padecen los sistemas especializados en la producción de leche, debido a la drástica disminución en la producción de leche. los costos ocasionados en el tratamiento, los descartes de vacas por recidivas y la eliminación de leche tratada por la presencia de residuos de antibióticos (inhibidores) dadas las dificultades que éstos causan en los procesos industriales (Bascon y Young, 1998). La mastitis puede presentarse en forma clinica o subclinica. La forma clínica se caracteriza por cambios visibles ocurridos en la ubre o en la leche. en muchos casos puede involucrar a la vaca e incluso ocasionarle la muerte.Ganado de leche-Ganadería lech

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. blaCMY−2−like was carried in 168 isolates, 52 carried blaCTX−M−2 group, 7 blaSHV, 5 a combination of blaCMY−2−like-blaSHV and 3 a combination of blaCMY−2−like-blaCTX−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 blaCMY−2 in 21, blaCTX−M−165 in 11 and blaSHV−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 blaCMY−2 and blaCTX−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

Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch.

BACKGROUND: Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting. METHODS: We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR. RESULTS: Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1-O3) represented 88.9% of all genomes, whereas capsule types were much more diverse. CONCLUSIONS: Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use meta-genomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.Peer reviewe

Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Prevalence, incidence and risk factors of subclinical mastitis in specialized dairies in Colombia

Introducción. La mastitis subclínica (MSC) es una de las principales enfermedades en bovinos; estudiar su epidemiología es fundamental para implementar programas de salud. Objetivo. Determinar la prevalencia, la incidencia y factores asociados a la mastitis subclínica en lecherías especializadas en Cundinamarca, Colombia. Materiales y Métodos. Se realizó un estudio observacional-analítico, de cohorte-prospectivo. Quince fincas se visitaron tres veces cada 56 días (septiembre-2019 a febrero-2020). En cada visita se realizó la prueba California (CMT), se evaluó suciedad de ubres y miembros posteriores de vacas lactantes y la rutina de ordeño. Se recolectó una muestra de leche por finca para determinar recuentos de células somáticas (RCS) y bacterias (RB). Modelos de regresión logística mixtos se usaron para determinar factores asociados con tener o adquirir MSC, y modelos lineales generalizados para determinar factores asociados a mayor prevalencia de MSC y RB. Se realizaron 960 CMT a 454 vacas. Resultados. Se realizaron 960 CMT a 454 vacas. La prevalencia de MSC (mediana) a nivel-hato fue 50 %, y estuvo directamente asociada con RCS y RB. La incidencia acumulada (mediana), a nivel-hato, para desarrollar una infección nueva y una crónica fue 42 % y 75 %, respectivamente. Factores asociados con tener MSC fueron: multiparidad (Odds ratio: OR≥2,35), lactancia tardía (OR=3,39), no presellar (OR=1,74) y sobreordeñar (OR=1,96). Factores que redujeron el riesgo de adquirir MSC fueron: tener <3 lactancias (OR≤0,29), lactancia temprana-media (OR≤0,32), segregación (OR=0,37) y presellar (OR=0,27). Factores asociados con la probabilidad de una mayor prevalencia de MSC fueron: no segregar (OR=2,42), ni presellar (OR=2,50). Factores asociados con elevados RB fueron: ubres sucias, tiempo de acción del presellador menor a 30 s y tener más de un ordeñador. Conclusión. Multiparidad, lactancia tardía (>180 dias en producción), no segregar, no presellar y sobreordeñar, fueron los factores que se asociaron con adquirir y tener mastitis subclínica, por lo tanto, se deben tener en cuenta en medidas de prevención y control.Introduction. Subclinical mastitis (SCM) is one of the main diseases in cattle; studying its epidemiology is essential to implement health programs. Objective. To determine the prevalence, incidence, and factors associated with subclinical mastitis in specialized dairies in Cundinamarca, Colombia. Materials and methods. An observational-analytical, prospective-cohort study was performed. Fifteen farms were visited three times every 56 days (September-2019 to February-2020). At each visit, the California test (CMT) was performed and dirtiness of udders and hind limbs of milking cows was evaluated; likewise, milking routine was evaluated. One milk sample per farm was collected to determine somatic cell counts (SCC) and bacteria count (BC). Logistic regression mixed models were used to determine factors associated with having or acquiring SCM, and generalized linear models to determine factors associated with the probability of a greater prevalence of SCM and BC. 960 CMT were performed on 454 cows. Results. A total of 960 CMT were performed on 454 cows. The median herd-level prevalence of SCM was 50 % and it was directly associated with SCC and BC. The median cumulative herd-level incidence of developing a new and a chronic infection of SCM was 42 % and 75 %, respectively. Factors associated with having SCM were: multiparous cows (Odds Ratio, OR≥2.35), late lactation (OR=3.39), no pre-dipping (OR=1.74), and over-milking (OR=1.96). Factors that reduced the risk of acquiring SCM were: having <3 lactations (OR≤0.29), early-mid lactation (OR≤0.32), segregating cows (OR=0.37), and pre-sealing (OR=0.27). Factors associated with the probability of a greater prevalence of SCM were: not segregating (OR=2.42) and not pre-dipping (OR=2.50). Factors associated with increased BC were: dirty udders, pre-sealer action time less than 30 s, and having more than one milker. Conclusion. Multiparous cows, late lactation (>180 days in production), not segregating, not pre-sealing, and over-milking, were factors associated with acquiring and having subclinical mastitis, therefore, they are key factors to consider in prevention and control measures.Universidad Nacional, Costa Rica.Escuela de Medicina Veterinari

Molecular diagnosis of Campylobacter in poultry chain intended for human consumption in Costa Rica.

El objetivo de este estudio fue determinar la presencia y la frecuencia de Campylobacter jejuni y Campylobacter coli, en la cadena de producción avícola en Costa Rica. Se evaluaron granjas, planta de proceso y puntos de venta del Gran Área Metropolitana. Para la detección y aislamiento de Campylobacter sp. se analizaron 84 muestras provenientes de la cadena avícola (24 muestras de carne de pollo tomadas en punto de venta, 20 enjuagues de carcasa y 40 de ciegos tomados en planta de beneficio), obtenidas en noviembre de 2012, siguiendo el protocolo ISO 10272-1:2006 modificado por el Departamento de Agricultura de Estados Unidos (USDA, por sus siglas en inglés). De las 84 muestras analizadas, 36 (42,8%) resultaron positivas para C. jejuni, y una (1,2%) para C. coli. La cantidad de muestras positivas según la Reacción en Cadena de Polimerasa (PCR), por tipo de muestra fue: para contenido cecal, 16 (n=40), para carcasas, 8 (n=20) y para punto de venta 12 (n=24). Dieciséis de las veinte granjas muestreadas fueron positivas. Hubo una alta frecuencia de Campylobacter en todos los puntos de la cadena muestreados, lo que podría estar asociado a modificaciones de parámetros relacionados con inocuidad en cada eslabón. El enfriamiento rápido y el uso de cloro en el agua en la planta de proceso, disminuyó la frecuencia de muestras positivas de Campylobacter spp.The aim of this study was to determine the presence and frequency of Campylobacter jejuni and Campylobacter coli in three levels of the poultry chain production in Costa Rica. The levels studied were farms, slaughterhouse/processing plant, and retails of the Great Metropolitan Area of Costa Rica. For detection and isolation of Campylobacter sp., 84 samples from the poultry chain (24 chicken meat samples at retail, 20 carcass rinses and 40 caecum contents taken at slaughterhouse), obtained in November 2012, following the ISO 10272-1:2006 protocol, USDA modified (United States Department of Agriculture). From the 84 samples analyzed, 36 (42.8%) were positive for C. jejuni, and one (1.2%) for C. coli. The quantity of positive samples per sample type, according to Polimerase Chain Reaction (PCR), was: for caecal content, 16 (n=40), for carcass, 8 (n=20) and retail, 12 (n=24). Sixteen of the twenty farms sampled were positive. A high frequency of Campylobacter spp. at all sample points of the production chain was determined, which could be associated with modification of parameters related to food safety in each link. Rapid cooling measures and the use of chlorine in the cooling water at the process plant collaborate to decrease the frequency of Campylobacter positive samples