Outbreak of human infections with uncommon Salmonella serotypes linked to pet bearded dragons, 2012-2014.

Reptiles are one of the fastest growing sectors in the United States pet industry. Reptile-associated salmonellosis (RAS) continues to be an important public health problem, especially among children. We investigated an outbreak of human Salmonella infections resulting from serotypes Cotham and Kisarawe, predominately occurring among children. An outbreak of illnesses was identified in persons with exposure to pet bearded dragon lizards. Human and animal health officials, in cooperation with the pet industry, conducted epidemiologic, traceback and laboratory investigations. Onsite sampling was conducted at two US breeding facilities, one foreign breeding facility, and a large pet retail chain. A total of 166 patients in 36 states were identified with illness onset dates from 02/2012-06/2014. The median patient age was 3 years (range, <1-79 years), 57% were aged ≤5 years, and 37% were aged ≤1 year. Forty-four patients (37%) were hospitalized, predominantly children. Sampling at breeding facilities and a national pet store chain resulted in isolation of outbreak serotypes at each facility; isolation proportions ranged from 2%-24% of samples collected at each facility.Epidemiologic, microbiologic and traceback evidence linked an outbreak of uncommon Salmonella serotypes to contact with pet bearded dragons. The high proportion of infants involved in this outbreak highlights the need to educate owners about the risk of RAS in children and the potential for household contamination by pet reptiles or their habitats. Strategies should be developed to improve breeding practices, biosecurity and monitoring protocols to reduce Salmonella in the pet reptile trade.

An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar.

How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost virus diversity. We develop an experimental protocol and computational tool, iVar, for using PrimalSeq to measure virus diversity using Illumina and compare the results to Oxford Nanopore sequencing. We demonstrate the utility of PrimalSeq by measuring Zika and West Nile virus diversity from varied sample types and show that the accumulation of genetic diversity is influenced by experimental and biological systems.

Endosymbiont interference and microbial diversity of the Pacific coast tick, Dermacentor occidentalis, in San Diego County, California.

The Pacific coast tick, Dermacentor occidentalis Marx, is found throughout California and can harbor agents that cause human diseases such as anaplasmosis, ehrlichiosis, tularemia, Rocky Mountain spotted fever and rickettsiosis 364D. Previous studies have demonstrated that nonpathogenic endosymbiotic bacteria can interfere with Rickettsia co-infections in other tick species. We hypothesized that within D. occidentalis ticks, interference may exist between different nonpathogenic endosymbiotic or nonendosymbiotic bacteria and Spotted Fever group Rickettsia (SFGR). Using PCR amplification and sequencing of the rompA gene and intergenic region we identified a cohort of SFGR-infected and non-infected D. occidentalis ticks collected from San Diego County. We then amplified a partial segment of the 16S rRNA gene and used next-generation sequencing to elucidate the microbiomes and levels of co-infection in the ticks. The SFGR R. philipii str. 364D and R. rhipicephali were detected in 2.3% and 8.2% of the ticks, respectively, via rompA sequencing. Interestingly, next generation sequencing revealed an inverse relationship between the number of Francisella-like endosymbiont (FLE) 16S rRNA sequences and Rickettsia 16S rRNA sequences within individual ticks that is consistent with partial interference between FLE and SFGR infecting ticks. After excluding the Rickettsia and FLE endosymbionts from the analysis, there was a small but significant difference in microbial community diversity and a pattern of geographic isolation by distance between collection locales. In addition, male ticks had a greater diversity of bacteria than female ticks and ticks that weren't infected with SFGR had similar microbiomes to canine skin microbiomes. Although experimental studies are required for confirmation, our findings are consistent with the hypothesis that FLEs and, to a lesser extent, other bacteria, interfere with the ability of D. occidentalis to be infected with certain SFGR. The results also raise interesting possibilities about the effects of putative vertebrate hosts on the tick microbiome.

Rapid bilateral intraocular cocktail sampling method for West Nile virus detection in dead corvids.

Corvids can be a sensitive indicator for West Nile virus (WNV) prevalence and are a component of many WNV surveillance programs. An improved sampling procedure using a bilateral intraocular cocktail (BIC) was developed for testing corvid carcasses for WNV. This new procedure was substantially faster than harvesting internal organs, required less specialized equipment and training, and yielded excellent diagnostic sensitivity.

Local veterinary diagnostic laboratory, a model for the one health initiative.

The San Diego County Animal Disease Diagnostic Laboratory (ADDL) is unique in its emphasis on protecting both human and animal health in San Diego County, and its use of interagency and community collaboration to create strong, effective public health programs. This article describes the ADDL core programs of avian and vector-borne disease surveillance, rabies testing, and animal abuse investigations and uses selected case studies to illustrate the need for a local veterinary diagnostic laboratory to safeguard the health of humans and animals. The ADDL serves as a role model for other local communities to develop vital public health partnerships to ensure a healthier community.

Discrimination between Francisella tularensis and Francisella-like endosymbionts when screening ticks by PCR.

The presence of Francisella-like endosymbionts in tick species known to transmit tularemia poses a potential diagnostic problem for laboratories that screen tick samples by PCR for Francisella tularensis. Tick samples initially considered positive for F. tularensis based on standard 16S rRNA gene PCR were found to be positive only for Francisella-like endosymbionts using a multitarget F. tularensis TaqMan assay (ISFtu2, tul4, and iglC) and 16S rRNA gene sequencing. Specificity of PCR-based diagnostics for F. tularensis should be carefully evaluated with appropriate specimen types prior to diagnostic use.