Zapata, S. | Search bioRxiv

bioRxiv2019

Salmonella grows massively and aerobically in fecal matter

The use of wastewater for irrigation and animal manure as fertilizer can cause transmission of intestinal pathogens, conditions frequently observed in Low- and Middle-Income Countries (LMICs). Here we tested the ability of Salmonella to grow in the fecal matter; we inoculated freshly isolated Salmonella strains (from chickens) in chicken fecal matter and incubated for 24, 48 and 72 hrs under aerobic and anaerobic conditions. We found that both Salmonella and E. coli multiplied massively in fecal matter outside a host for 72 hrs, being their growth higher in aerobic conditions. Our results have critical implications in waste management, as we demonstrate that aerobic treatments may not be the best to reduce the number of Salmonella in the environment.

microbiology↗

bioRxiv2019

Oropouche virus cases identified in Ecuador using an optimised rRT-PCR informed by metagenomic sequencing

Oropouche virus (OROV) is responsible for outbreaks of Oropouche fever in parts of South America. We recently identified and isolated OROV from a febrile Ecuadorian patient, however, a previously published rRT-PCR assay did not detect OROV in the patient sample. A primer mismatch to the Ecuadorian OROV lineage was identified from metagenomic sequencing data. We report the optimisation of an rRT-PCR assay for the Ecuadorian OROV lineage, which subsequently identified a further five cases in a cohort of 196 febrile patients. We isolated OROV via cell culture and developed an algorithmically-designed primer set for whole-genome amplification of the virus. Metagenomic sequencing of the patient samples provided OROV genome coverage ranging from 68 - 99%. The additional cases formed a single phylogenetic cluster together with the initial case. OROV should be considered as a differential diagnosis for Ecuadorian patients with febrile illness to avoid mis-diagnosis with other circulating pathogens.

genomics↗