This report documents the emergence of macrolide-resistant Bordetella pertussis (MRBP) during the 2025 pertussis outbreak in Peru. Surveillance screening of 68 B. pertussis–positive nasopharyngeal swab samples by direct PCR detected the A2047G mutation in the 23S rRNA gene in 21 samples (31%). Whole-genome sequencing of seven culture-positive isolates showed that all belonged to sequence type ST2 and carried genetic markers of the emerging MR-MT28 lineage, including the prn150 allele. Genomic analysis identified at least two genetically distinct MR-MT28 sublineages among isolates from Peru, consistent with multiple international introductions. The findings support strengthening surveillance for macrolide-resistant pertussis to inform public health control strategies.
Context and outbreak magnitude
Peru reported a large pertussis outbreak concentrated in 2024–2025. National incidence rose from 3.9 cases per 1 million inhabitants in 2023 to 7.4 cases per 1 million in 2024 and reached 57.5 cases per 1 million by August 2025. By the end of 2025, surveillance recorded 4,976 cumulative cases and 76 deaths, with the Loreto region accounting for the majority of cases and deaths. Vaccination coverage in certain affected areas, including Indigenous communities in Datem del Marañón, remained suboptimal.
Specimen collection and molecular screening
In early 2025, investigators screened 68 nasopharyngeal swab specimens that were positive for B. pertussis. Patients’ ages ranged from 1 month to 39 years, with a median age of 3 months. Direct PCR targeting the A2047G mutation in the 23S rRNA genes was used to detect macrolide resistance. The A2047G mutation was identified in 21 of 68 samples (31%). Patients infected with MRBP were significantly younger than those infected with macrolide-susceptible strains (median 3.6 vs 36.1 months; p = 0.007). No significant differences in sex or vaccination status were observed between groups based on the available data. Most MRBP infections occurred in infants under 6 months of age (62%).
Geographic distribution and clinical management
MRBP cases were detected across multiple regions, including Lima (11 cases), Cusco (4), Arequipa (3), Ancash (1), Loreto (1), and Puno (1). Treatment information was available for 16 patients; among these, 14 (88%) received azithromycin. The report does not provide further clinical outcome details for individual patients beyond age distribution and treatment data in the screened subset.
Culture, phenotypic susceptibility, and genomics
From the 68 PCR-positive samples, seven culture-positive B. pertussis isolates were obtained; six isolates were collected in 2025 and one in late 2024 (isolate tf518-24). Phenotypic susceptibility testing demonstrated resistance in all seven isolates, with no zones of inhibition observed for erythromycin or azithromycin, indicating high-level macrolide resistance.
Whole-genome sequencing was performed on all seven MRBP isolates. All sequenced isolates were assigned to sequence type ST2 and clonal complex ST2. Six isolates shared a common virulence-associated allelic profile: ptxP3/ptxA1/ptxB1/ptxC4/fhaB1/fim2-1/fim3-1; one isolate (tf098–25) carried the ptxP29 promoter allele while retaining the other alleles in this profile. All isolates carried the prn150 allele, a marker noted in the emerging MR-MT28 lineage. Three isolates (tf518-24, tf120-25, and tf098-25) had IS481-mediated disruption of prn consistent with a pertactin-deficient genotype; no inactivating mutations in the ptx operon or fhaB were identified.
Phylogenetic placement and diversity
Expanded genome-wide single-nucleotide polymorphism phylogenetic analysis, incorporating globally representative MRBP genomes, placed the Peruvian isolates within the emerging MR-MT28 lineage and identified previously reported markers such as the A2047G mutation and the BP0685 G1959A substitution. The seven Peruvian isolates did not form a single monophyletic cluster: three isolates clustered within the PG1 sublineage and showed prn disruption, while four clustered in a separate MR-MT28-other group and retained intact prn coding sequences despite carrying the prn150 allele. This distribution indicates at least two genetically distinct MR-MT28 sublineages present in Peru.
Limitations of data presented
The screening covered 68 B. pertussis–positive specimens and yielded seven cultured isolates subjected to whole-genome sequencing. The report provides limited clinical outcome data beyond age distribution and treatment in a subset of patients. Additional details about clinical severity, treatment responses, and wider temporal sampling were not reported in the provided source text.
This investigation documents the emergence and geographic spread of macrolide-resistant Bordetella pertussis during the 2025 pertussis outbreak in Peru and confirms circulation of the emerging MR-MT28 lineage in Latin America. Genomic analyses identified more than one genetically distinct MR-MT28 sublineage in Peru, including a PG1-associated group with pertactin deficiency, consistent with international diversification and dissemination of this lineage rather than a single introduction event.
The data indicate that MRBP disproportionately affected very young infants in the sampled cohort, with most MRBP infections occurring in those under 6 months of age. Although azithromycin was commonly used in the reported subset of treated patients, the cultured isolates demonstrated phenotypic resistance to erythromycin and azithromycin. The findings underscore the need to strengthen laboratory surveillance for macrolide-resistant pertussis to inform treatment decisions and public health control strategies.
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