Draft Genome Sequences of Vibrio cholerae Non-O1, Non-O139 Isolates from Common Tern Chicks (Sterna hirundo) following a Mass Mortality Event

Vibrio cholerae is an inhabitant of aquatic environments worldwide. Here, we report the draft genome sequences of eight V. cholera non-O1, non-O139 isolates that were recovered from the corpses of two seabird chicks (common terns) following a mass mortality event in a German breeding colony in 2019.

T he presence of Vibrio cholerae in seabirds has been well known for many years (1,2). Migrating birds are regarded as vectors for long-distance transport of these bacteria (3). Usually, the bacteria are regarded as commensals, while diseases of birds caused by V. cholerae are rarely reported.
In July 2019, a high chick mortality rate was observed in a colony of common terns (Sterna hirundo) in the saltmarshes of Neufelderkoog (District Dithmarschen) in the River Elbe Estuary (53°53937.00N, 8°58955.210E) (4). There, the seabird brood of 1 year (;1,500 chicks) died within 1 week shortly before they were able to fly. To determine the cause of death, necropsies and microbiological investigations were conducted on two chick corpses. Tissue samples were taken from inner organs, and the samples were cultivated at 37°C on Columbia sheep blood agar (Thermo Fisher Scientific, Berlin, Germany) and MacConkey agar (Merck, Darmstadt, Germany) for 24 h and 48 h, respectively. Visible colonies were investigated using matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MALDI Biotyper; Bruker Daltonik, Bremen, Germany). V. cholerae non-O1, non-O139 isolates were recovered from liver, kidney, heart, small intestine, and lung, raising the possibility that these bacteria could be involved in the death of the birds. Herring as the sole feed for the chicks were suspected as a source of the infection. One V. cholerae isolate from each organ (eight isolates in total) ( Table 1) was cultured on thiosulfate-citrate-bile-sucrose agar (Thermo Fisher Scientific) and ChromID Vibrio agar (bioMérieux, Marcy-l'Etoile, France) and sent to the Federal Institute for Risk Assessment.
Automated de novo assembly (SPAdes v3.5.49) and genome annotation were performed using PATRIC (release 3.5.39) (6). Default parameters were routinely used for all       software tools. Further information on software versions and parameters is given in Table 1. Bioinformatic analysis was conducted with the specified tools of the Center for Genomic Epidemiology (http://www.genomicepidemiology.org) and PGAP (National Center for Biotechnology Information) (7). Prophage prediction was performed with PHASTER (accessed 9 June 2019) (8). Important phenotypic and genotypic features of the V. cholerae genomes are summarized in Table 1. Determination of antimicrobial resistance phenotypes was performed as described previously (9). Because the genomes exhibited ,19 single-nucleotide polymorphisms (SNPs) in 4,072,405 positions (representing nearly 100% of the genomes), the isolates were suggested to be clonal.
In silico prediction of phage-associated sequences revealed the presence of up to two prophages. One prophage sequence is similar to that of the linear Vibrio satellite phage KSF-1phi (GenBank accession number AY714348) (10). The second prophage possesses sequences matching those of the phage myovirus K139 (GenBank accession number NC_003313) (11).
The genomes of the seabird isolates possess an SXT/R391-like integrative conjugative element (ICE) that is related to a 103-kb ICEVchBan8 element (GenBank accession number JQ345361) of a human pathogenic V. cholerae O37 strain (12). This ICE encodes potential virulence factors in a hot spot region of 45 kb, which might have contributed to the premature deaths of the young birds.
Data availability. Accession numbers for whole-genome sequences and raw sequencing reads (SRA accession numbers) are listed in Table 1.