Department of General Services

We report on five SARS-CoV-2 congregate setting outbreaks at U.S. Operation Allies Welcome Safe Havens/military facilities. Outbreak data were collected, and attack rates were calculated for various populations. Even in vaccinated populations, there was rapid spread, illustrating the importance of institutional prevention and mitigation policies in congregate settings.

Monkeypox is a viral zoonotic disease endemic in Central and West Africa. In May 2022, dozens of non-endemic countries reported hundreds of monkeypox cases, most with no epidemiological link to Africa. We identified two lineages of monkeypox virus (MPXV) among two 2021 and seven 2022 US monkeypox cases: the major 2022 outbreak variant called B.1 and a minor contemporaneously sampled variant called A.2. Analyses of mutations among these two variants revealed an extreme preference for GA-to-AA mutations indicative of human APOBEC3 cytosine deaminase activity among Clade IIb MPXV (previously West African, Nigeria) sampled since 2017. Such mutations were not enriched within other MPXV clades. These findings suggest that APOBEC3 editing may be a recurrent and a dominant driver of MPXV evolution within the current outbreak.

Nearly all cases of melioidosis in the continental United States are related to international travel to areas to which Burkholderia pseudomallei, the bacterium that causes melioidosis, is endemic. We report the diagnosis and clinical course of melioidosis in a patient from the United States who had no international travel history and the public health investigation to determine the source of exposure. We tested environmental samples collected from the patient’s home for B. pseudomallei by PCR and culture. Whole-genome sequencing was conducted on PCR-positive environmental samples, and results were compared with sequences from the patient’s clinical specimen. Three PCR-positive environmental samples, all collected from a freshwater home aquarium that had contained imported tropical fish, were a genetic match to the clinical isolate from the patient. This finding suggests a novel route of exposure and a potential for importation of B. pseudomallei, a select agent, into the United States from disease-endemic areas.

BackgroundProcessing and analyzing whole genome sequencing (WGS) is computationally intense: a single Illumina MiSeq WGS run produces ~ 1 million 250-base-pair reads for each of 24 samples. This poses significant obstacles for smaller laboratories, or laboratories not affiliated with larger projects, which may not have dedicated bioinformatics staff or computing power to effectively use genomic data to protect public health. Building on the success of the cloud-based Galaxy bioinformatics platform (http://galaxyproject.org), already known for its user-friendliness and powerful WGS analytical tools, the Center for Food Safety and Applied Nutrition (CFSAN) at the U.S. Food and Drug Administration (FDA) created a customized ‘instance’ of the Galaxy environment, called GalaxyTrakr (https://www.galaxytrakr.org), for use by laboratory scientists performing food-safety regulatory research. The goal was to enable laboratories outside of the FDA internal network to (1) perform quality assessments of sequence data, (2) identify links between clinical isolates and positive food/environmental samples, including those at the National Center for Biotechnology Information sequence read archive (https://www.ncbi.nlm.nih.gov/sra/), and (3) explore new methodologies such as metagenomics. GalaxyTrakr hosts a variety of free and adaptable tools and provides the data storage and computing power to run the tools. These tools support coordinated analytic methods and consistent interpretation of results across laboratories. Users can create and share tools for their specific needs and use sequence data generated locally and elsewhere.ResultsIn its first full year (2018), GalaxyTrakr processed over 85,000 jobs and went from 25 to 250 users, representing 53 different public and state health laboratories, academic institutions, international health laboratories, and federal organizations. By mid-2020, it has grown to 600 registered users and processed over 450,000 analytical jobs. To illustrate how laboratories are making use of this resource, we describe how six institutions use GalaxyTrakr to quickly analyze and review their data. Instructions for participating in GalaxyTrakr are provided.ConclusionsGalaxyTrakr advances food safety by providing reliable and harmonized WGS analyses for public health laboratories and promoting collaboration across laboratories with differing resources. Anticipated enhancements to this resource will include workflows for additional foodborne pathogens, viruses, and parasites, as well as new tools and services.

BackgroundAntimicrobial resistance (AMR) in foodborne pathogens of animal origin, including non-typhoidal Salmonella (NTS) are a public health concern. Pennsylvania conducts integrated surveillance for AMR in NTS isolates from human and animal sources in collaboration with the National Antimicrobial Resistance Monitoring System (NARMS).MethodsDuring 2009-2014, Salmonella enterica isolates from various types of meat purchased from randomly selected retail outlets in southeastern Pennsylvania were analyzed by pulsed-field gel electrophoresis (PFGE). We compared PFGE patterns from meat with clinical isolates in the Pennsylvania surveillance database. All meat isolates and a subset of matched clinical isolates were tested for susceptibility to antimicrobial agents. Eleven isolates with indistinguishable PFGE patterns were analyzed by whole genome sequencing (WGS). Sequence data were uploaded to the FDA’s GalaxyTrakr platform for quality assessment, genome assembly, AMR gene detection, and phylogenetic inference via single-nucleotide polymorphism (SNP) analysis.ResultsPFGE patterns of 86 (48.6%) of 177 meat isolates had PFGE matches to 1,665 clinical isolates; 40 distinct PFGE patterns were represented among the shared patterns. Seventeen (43%) of the 40 shared PFGE patterns (with ≥1 isolate(s) from both sources) were considered multi-drug resistant (MDR). Among the 48 S. Berta pattern JAXX01.0001 isolates, 5 (10.9%) and 2 (100%) from human and meat sources respectively were MDR including resistance to amoxicillin and ceftriaxone. WGS analysis of one isolate from ground turkey meat (PNUSAS061602) was genetically related to clinical isolates including two within 9 and 11 SNPs [Figure]. Presence of genes that hydrolyze extended spectrum cephalosporins (ESC), [blaCMY, blaHERA, or blaTEM], was identified in eight (two meat and six clinical) isolates. One meat isolate was resistant to six antibiotics including ceftriaxone.Figure 2. Single nucleotide polymorphism (SNP) distance matrix showing relatedness in non-typhoidal Salmonella isolates from retail meat (n=2) and human (n=9) sources — Pennsylvania, 2010-2014. One S Berta from retail meat was separated from two clinical two clinical isolates by 9 and 11 SNPs. Second isolate from meat was separated from those associated with human infections by 14 (n=1), 17 (n=1) and ≥20 (n=7).ConclusionWGS analysis revealed clinically relevant ESCs genes in closely related S. Berta isolates from human and animal sources. Presence of these genes in NTS highlights the need for enhanced One-Health surveillance and judicious use of antibiotics in humans and food-animal production.DisclosuresAll Authors: No reported disclosures

Vibrio vulnificus is a Gram-negative bacterium and an opportunistic pathogen that can cause septicemia or necrotizing fasciitis. Here, we report the draft genome sequences of 42 environmental V. vulnificus strains collected from the northern Gulf of Mexico. These data will allow for more robust comparisons between clinical and environmental strains.

We describe the efficacy of enhanced infection control measures, including those recommended in the Centers for Disease Control and Prevention's 2012 carbapenem-resistant Enterobacteriaceae (CRE) toolkit, to control concurrent outbreaks of carbapenemase-producing Enterobacteriaceae (CPE) and extensively drug-resistant Acinetobacter baumannii (XDR-AB). Before-after intervention study. Fifteen-bed surgical trauma intensive care unit (ICU). We investigated the impact of enhanced infection control measures in response to clusters of CPE and XDR-AB infections in an ICU from April 2009 to March 2010. Polymerase chain reaction was used to detect the presence of blaKPC and resistance plasmids in CRE. Pulsed-field gel electrophoresis was performed to assess XDR-AB clonality. Enhanced infection-control measures were implemented in response to ongoing transmission of CPE and a new outbreak of XDR-AB. Efficacy was evaluated by comparing the incidence rate (IR) of CPE and XDR-AB before and after the implementation of these measures. The IR of CPE for the 12 months before the implementation of enhanced measures was 7.77 cases per 1,000 patient-days, whereas the IR of XDR-AB for the 3 months before implementation was 6.79 cases per 1,000 patient-days. All examined CPE shared endemic blaKPC resistance plasmids, and 6 of the 7 XDR-AB isolates were clonal. Following institution of enhanced infection control measures, the CPE IR decreased to 1.22 cases per 1,000 patient-days (P = .001), and no more cases of XDR-AB were identified. Use of infection control measures described in the Centers for Disease Control and Prevention's 2012 CRE toolkit was associated with a reduction in the IR of CPE and an interruption in XDR-AB transmission.