Bacterial Communities Associated with Lesions of Shell Disease in the American Lobster,Homarus americanusMilne-Edwards

Shell disease in Crustacea is a widely recognized syndrome having a polymicrobial etiology, and manifesting itself as lesions of the shell with a variable structure and shell location. We characterized major members of bacterial communities in epizootic shell disease lesions of the American lobster (Homarus americanus, Milne Edwards) and compared these communities with the ones found in study cases of impoundment and enzootic shell disease. Bacteria belonging to several Flavobacteriaceae genera (Aquimarina, Tenacibaculum, Polaribacter, Maribacter, Cellulophaga) within the phylum Bacteroidetes appear to have particular attraction to lobster lesions. The most prominent Bacteroidetes in lobster lesions were representatives of the genus Aquimarina sp., but only Aquimarina ‘homaria’ was detected in all analyzed lesions of epizootic, impoundment, and enzootic shell disease. It was found on 45% of surfaces unaffected by shell disease, but in smaller numbers compared with lesions. Alphaproteobacteria represent the most diverse class of proteobacteria found in both lesions and on unaffected surfaces. Three bacteria of this class appear to be ubiquitous in shell disease lesions, but only one specific alphaproteobacterium tentatively assigned to the genus Thalassobius (herein designated as ‘Thalassobius’ sp.) was present in all analyzed lesions of epizootic, impoundment, and enzootic shell disease. A ubiquitous gammaproteobacterium called ‘Candidatus Homarophilus dermatus’ was also prevalent in lesions, but just as commonly it was associated with surfaces unaffected by shell disease. The bacteria A. ‘homaria’ and ‘Thalassobius’ sp. are dominant and appear obligatory in lobster shell lesions, and are only occasionally detected on unaffected surfaces, which serve as intermediate reservoirs for the two potential pathogens. Therefore, these two bacteria stand out as potential shell-disease pathogens

Implementation of a high-throughput whole genome sequencing approach with the goal of maximizing efficiency and cost effectiveness to improve public health

ABSTRACTThis manuscript describes the development of a streamlined, cost-effective laboratory workflow to meet the demands of increased whole genome sequence (WGS) capacity while achieving mandated quality metrics. From 2020 to 2021, the Wadsworth Center Bacteriology Laboratory (WCBL) used a streamlined workflow to sequence 5,743 genomes that contributed sequence data to nine different projects. The combined use of the QIAcube HT, Illumina DNA Prep using quarter volume reactions, and the NextSeq allowed the WCBL to process all samples that required WGS while also achieving a median turn-around time of 7 days (range 4 to 10 days) and meeting minimum sequence quality requirements. Public Health Laboratories should consider implementing these methods to aid in meeting testing requirements within budgetary restrictions.IMPORTANCEPublic Health Laboratories that implement whole genome sequencing (WGS) technologies may struggle to find the balance between sample volume and cost effectiveness. We present a method that allows for sequencing of a variety of bacterial isolates in a cost-effective manner. This report provides specific strategies to implement high-volume WGS, including an innovative, low-cost solution utilizing a novel quarter volume sequencing library preparation. The methods described support the use of high-throughput DNA extraction and WGS within budgetary constraints, strengthening public health responses to outbreaks and disease surveillance