PCR Testing Improves Detection of Fleaborne Typhus in Los Angeles County, Extending Diagnostic Window to 15 Days
Key Insights
A Los Angeles County study found that 71% of low-titer positive serology specimens from patients with illness consistent with fleaborne typhus (search) (FBT) were PCR-positive for Rickettsia typhi (search), underscoring the value of molecular testing for diagnosis and case detection.
Most PCR-positive specimens (91%) were collected within 10 days of illness onset, with some positive up to 15 days, suggesting the previously recommended 1-week PCR testing window is too restrictive.
All 81 PCR-positive specimens tested positive for R. typhi and none for R. felis, reinforcing that R. typhi is the primary etiologic agent of FBT in California.
A study conducted by the Los Angeles County Department of Public Health (search) (LACDPH) demonstrates that PCR testing substantially improves case detection of fleaborne typhus (search) (FBT), a disease caused by Rickettsia typhi (search). The research, published in the CDC's Emerging Infectious Diseases journal, analyzed specimens collected between 2022 and 2024 and found that most low-titer positive serology specimens from patients with clinically compatible illness represented true R. typhi infections.
In the study, most (71%) of the initial low-titer positive serology specimens obtained from patients with illness consistent with FBT were PCR-positive for R. typhi. That finding highlights the effectiveness of using PCR testing for clinical diagnosis and case detection of FBT. Unfortunately, Rickettsia sp. PCR testing has not been widely implemented because of the resources and laboratory expertise required. In the United States, rickettsial PCR testing remains largely limited to specialized public health laboratories and surveillance activities rather than routine clinical use.
Extending the Diagnostic Window
A key finding of the study concerns the timing of PCR positivity. Most (91%) PCR-positive specimens were collected within 10 days after illness onset, with some positive up to 15 days. Those results suggest that the previously recommended 1-week window for FBT PCR testing might be too restrictive. Furthermore, the results suggest that rickettsial nucleic acids might persist in the bloodstream for longer than previously recognized, thereby extending the diagnostic window for molecular testing. Expanding the testing window beyond the first week could improve case detection and provide a more accurate understanding of the timing of rickettsial nucleic acid persistence in patients.
Identifying the Primary Etiologic Agent
All 81 PCR-positive specimens in this study tested positive for R. typhi and none for R. felis. That finding reinforces a previous conclusion that R. typhi is the primary etiologic agent of FBT in California. Historically, both R. typhi and R. felis have been considered potential causes of FBT, including in urban Los Angeles, where both pathogens have been demonstrated to circulate in rat populations and associated fleas. The absence of R. felis in the PCR-positive specimens challenges previous assumptions about the involvement of different rickettsial species in FBT infection. Recognizing R. typhi as the principal agent is critical for interpreting the changing epidemiology of FBT, including increases in case numbers, geographic expansion, and evolving risk factors.
Serologic Testing Variability
The study demonstrated variability in serologic testing results between commercial and public health laboratories. About 93% of the low-titer positive specimens obtained from commercial laboratories for repeat serologic testing had higher titers at the Los Angeles County Public Health Laboratory (LACPHL). That result is a known major weakness of serologic testing, and the results align with existing evidence that the reading of IFA slides is prone to subjectivity. In addition, the lack of standardized IFA reagents, protocols, and criteria for test interpretation might account for titer variability between laboratories.
In practice, it is not feasible for public health laboratories to repeat serologic testing of all commercial low-titer positive specimens. Obtaining confirmatory convalescent serology specimens is also not practical because many patients will have recovered by the recommended 10–14-day return window and no longer need medical care, or might face financial barriers preventing them from seeking further care. Rickettsia sp. serologic testing is also subject to high cross-reactivity between Rickettsia species. Because FBT manifests as a nonspecific illness, making PCR testing commercially available would enable rapid and accurate diagnosis of FBT and confirmation of Rickettsia species.
The Role of IgM Testing
The study underscores the importance of keeping IgM test results as part of the laboratory criteria in the FBT surveillance case definition. Studies suggest that Rickettsia IgM titers are less reliable and have limited utility compared with IgG titers because they have lower specificity and do not rise much earlier than IgG titers. Those studies prompted the exclusion of IgM test results from the California Department of Public Health (CDPH) and national FBT case definition laboratory criteria in 2025. In this study, 48 (87%) of 55 patient specimens that had only IgM and no IgG detected in the initial testing by a commercial laboratory were found to be PCR-positive through public health testing. Those specimens were likely collected earlier in the disease course before a measurable rise in IgG titers occurred and when PCR testing is most sensitive. Those cases (n = 48) would have been misclassified if IgM testing results were not included in the protocol.
Treatment Patterns and Clinical Presentation
Most (91%) cases in this study were appropriately treated with doxycycline, demonstrating that clinicians are correctly suspecting FBT at the time of treatment initiation and ordering diagnostic testing. Furthermore, 63% of patients received doxycycline before or on the same day of specimen collection, indicating that patients with FBT in the differential diagnosis are being treated empirically before serology results are reported. That treatment pattern is encouraging because of the variability of rickettsial serology testing and aligns with public health messaging on the importance of early doxycycline initiation.
The study population is representative of the overall FBT cases. The case demographics did not differ from those of high-titer positive cases. However, low-titer positive cases manifested with nausea or vomiting, rash, and thrombocytopenia more often than high-titer positive cases did. Low-titer positive cases were also more likely to be seen earlier in their illness, which might explain the differences in symptoms observed.
Surveillance Impact
Nearly all (99%) specimens that were submitted for additional testing returned with results that met CDPH surveillance criteria for a probable or confirmed FBT case. Because of this testing protocol result, LACDPH has added 113 probable or confirmed cases of FBT from April 2022–December 2024 to overall case counts. Suspected cases are typically excluded from surveillance case counts publicly reported by public health jurisdictions. Public health jurisdictions that use a minimum titer to initiate case investigations might overlook those low-titer positive cases, resulting in underreporting of FBT case counts.
Study Limitations
The first limitation of the study was the use of residual serum specimens for PCR testing, rather than whole blood or plasma, which are better suited for molecular detection of Rickettsia. Because Rickettsia are obligate intracellular organisms, their nucleic acids are more concentrated in cellular components and plasma compared with serum, where clot formation removes most cells and might reduce detectable DNA. Of note, one case had both serum and plasma from the same collection date available for testing; in that case, R. typhi nucleic acids were detected in the plasma but not the serum, underscoring the effect of specimen type on PCR sensitivity.
Second, the true effect of FBT in Los Angeles County is likely underestimated, and the findings might not fully represent the extent of disease transmission in the community. The reporting of FBT test results to LACDPH by laboratories and healthcare providers could be incomplete, resulting in possible missed cases. Patients with mild FBT symptoms who might not have sought care, were not tested, or were tested very early in their disease course, when antibody titers were undetectable, were not captured in this analysis. Because the study was geographically restricted to Los Angeles County, the findings might not be representative of the general population of the United States.
Third, although LACDPH attempted to obtain all medical records relevant to the patients' illness with FBT, it is possible that some follow-up visits were not captured, resulting in incomplete information on doxycycline treatment. Fourth, the sample size for subgroup comparisons was relatively small, reducing statistical power and increasing the likelihood of random error. Last, not all specimens could be obtained for analysis, as commercial laboratories generally retain specimens for a limited time, and delays in obtaining medical records meant that some specimens were discarded before they could be retrieved.
Retrospective testing of specimens by using rRNA did not change the conclusion that most low-titer specimens were PCR-positive. The rRNA assay did detect three additional PCR-positive specimens that had previously returned unsatisfactory, indeterminate, or negative results by the DNA-based assays. Those results would have changed the classification of three cases from probable to confirmed, though those cases could not be reclassified in surveillance data because case investigations are finalized after the completion of each calendar year.
The authors conclude that enhanced public health laboratory testing, like that conducted in the study, is effective for accurately classifying cases for comprehensive case surveillance. However, that approach is not sustainable as routine practice and further strains limited public health resources. Wider commercial availability of Rickettsia PCR testing and other new technologies could substantially enhance both clinical diagnostic capacity and the understanding of true disease effects. The resurgence of FBT in Los Angeles County and other areas of the United States highlights the importance of reexamining the current diagnostic protocols being used in clinical settings and public health surveillance.