When disease outbreaks move quickly, public health laboratories need answers quickly too—but often without more staff or money. This study found a way to process thousands of bacterial genomes while keeping the results dependable and affordable. Across public health work, laboratories are continually challenged to meet the demand for increased testing capacity, often in the absence of increased funding.

During the COVID-19 pandemic, instrumentation resources and testing staff were strained, with up to ninety percent of WCBL staff reassigned to the response, alongside laboratory supply shortages. So the laboratory developed a cost-effective, streamlined workflow for handling more whole-genome testing.

Its backbone was coordination across multiple units, allowing large numbers of bacterial samples to be handled together. The central problem was a balancing act: public health laboratories had to process more bacterial samples while keeping costs under control.

The goal was a method that could sequence many kinds of bacteria cost-effectively. The solution included a low-cost way to prepare samples using only a quarter of the usual preparation volume. Together, the methods supported high-volume testing within budget limits, strengthening outbreak response and disease surveillance.

The workflow first prepared two broad kinds of bacteria so they could enter one high-throughput DNA extraction run. An automated platform then handled the extraction, rather than requiring each sample to be processed separately by hand. Different bacterial groups received separate pretreatment, then were combined in one high-throughput extraction run, making it possible to process both types together.

The laboratory compared several DNA extraction platforms. The high-throughput platform required the least hands-on technician and instrument time for a large run and was also the most cost-effective among the platforms used. The lower-cost preparation and sequencing approach cost sixty-eight dollars per sample.

The selected combination of extraction, preparation, and sequencing cost seventy-eight dollars and thirty-nine cents per bacterial sample without sacrificing data quality. From 2020 to 2021, the laboratory sequenced five thousand seven hundred forty-three genomes that contributed sequence data to nine different public health projects.

Most of those genomes contributed to CDC PulseNet, followed by FDA GenomeTrakr and the Antibiotic Resistance Laboratory Network, among the projects listed. The sequencing included a wide variety of bacterial organisms: Salmonella enterica was most common, followed by Listeria monocytogenes, Escherichia coli, Klebsiella pneumoniae, and others.

The laboratory’s sequencing workload grew sharply from 2020 to 2021, reaching 3,698 genomes compared with 2,045 the year before. That rise puts the faster turnaround in context: the laboratory was handling substantially more work while responding to the pandemic. Monthly workload showed a marked increase from 2020 to 2021.

The laboratory sequenced two thousand forty-five genomes in 2020 and three thousand six hundred ninety-eight in 2021. The increase likely reflected the effects of the COVID-19 pandemic, when most staff were reassigned to COVID-19 response efforts and research projects were suspended.

The system therefore had to keep operating while normal laboratory work was disrupted. The median turnaround time from scheduling a bacterial isolate for DNA extraction to having genome data ready for analysis was seven days, with results available within four to ten days.

That improved turnaround by about two days compared with the prior workflow. The faster timing came from several changes: the high-throughput sequencing runs took less time, one dedicated person processed all samples, and the schedule was more regular.

If volume was high, two runs could be performed to keep the turnaround time on target. The study's practical lesson is that public health laboratories should choose extraction and sequencing systems based on the amount of testing they expect.

Cooperation between laboratory units can also make larger batches possible and reduce costs. Even with weekly batching for DNA extraction and sequencing, whole genome sequencing data were available for analysis within four to ten days.

A coordinated, high-volume workflow made bacterial genome testing less expensive, more regular, and available within days. That can help public health teams track outbreaks and disease threats when resources are stretched.