Life sciences · Journal article

Global genomic surveillance uncovers emergence and spatiotemporal patterns of World Health Organization priority antibiotic resistance in invasive Salmonella

Nature Communications · August 17, 2026

Preliminary Why this matters to you Expert discussion

Early or partial results. Treat as a signal, not a conclusion.

AI Summary

This is a global retrospective genomic surveillance study of 7,691 invasive Salmonella isolates spanning 1954–2024, documenting resistance prevalence and temporal trends to WHO-priority antibiotics. The work quantifies the burden and geographic spread of resistance but does not measure clinical outcomes or intervention efficacy, and acknowledges significant surveillance gaps in Africa and South America.

What was studied

Retrospective global longitudinal genomic epidemiology study. Invasive Salmonella isolates from national surveillance and public repositories; no patient-level clinical data reported. Geographic scope spans 77 countries; however, surveillance is inadequate in African and South American regions.. n = 7,691. 77 countries globally; specific regional breakdown and counts not provided. Study notes inadequate surveillance in Africa and South America..

Key findings

37.7% of 77 countries identified at least one isolate with ciprofloxacin resistance or decreased susceptibility Overall 7.39% of 7,691 isolates resistant or decreased susceptible to ciprofloxacin; 7.91% to 3rd-generation cephalosporins; 4.23% to fosfomycin; 0.79% to azithromycin Azithromycin resistance is increasing globally, as is resistance or decreased susceptibility to ciprofloxacin, 3GCs, and 4GCs

Safety

No clinical outcomes (morbidity, mortality, treatment failure) reported; purely genomic and prevalence data.

Who this may help

Clinicians and public health authorities should use this descriptive data to understand the global epidemiology and emerging resistance patterns in invasive Salmonella, informing empirical therapy choices and surveillance priorities. However, the absence of clinical outcomes and incomplete geographic coverage limits its direct application to treatment guidelines without supporting mechanistic or clinical trial evidence.

Plain-language summary

A large retrospective genomic surveillance study describing resistance prevalence and trends across 7,691 isolates, but without clinical outcomes, intervention comparisons, or mechanistic validation to support practice-changing or strong evidence.

Study design

As stated by the source record.

Methods7,691 invasive Salmonella isolates derived from national surveillance and publicly available datasets were analysed between 1954 and 2024. Genomic sequencing and resistance profiling were performed to identify WHO-priority antibiotic resistance markers. Isolates were stratified by country (77 total) and by antibiotic class (ciprofloxacin, 3rd- and 4th-generation cephalosporins, azithromycin, fosfomycin, colistin). Prevalence was calculated as the proportion of resistant or decreased-susceptibility isolates per antibiotic and per country; temporal and geographic patterns were mapped.

DesignRetrospective global longitudinal genomic epidemiology study

PopulationInvasive Salmonella isolates from national surveillance and public repositories; no patient-level clinical data reported. Geographic scope spans 77 countries; however, surveillance is inadequate in African and South American regions.

Sample size7,691

Setting77 countries globally; specific regional breakdown and counts not provided. Study notes inadequate surveillance in Africa and South America.

Reported figures

Quoted from the source exactly as published.

Sample size7691

Countries surveyed77

Ciprofloxacin resistance or decreased susceptibility prevalence7.39%

3rd-generation cephalosporin resistance or decreased susceptibility prevalence7.91%

Fosfomycin resistance prevalence4.23%

Azithromycin resistance prevalence0.79%

Countries with ciprofloxacin resistance/decreased susceptibility29 of 77 (37.7%)

Countries with colistin resistance10 of 77 (13.0%)

Clinical bottom line

Caveats

No clinical outcomes (morbidity, mortality, treatment failure) reported; purely genomic and prevalence data.
Retrospective aggregation from heterogeneous national and public sources; no quantitative assessment of reporting bias or surveillance methodology differences.
Acknowledged inadequate surveillance coverage in African and South American regions limits global representativeness.
No statistical testing of trend significance or confidence intervals around prevalence estimates provided; temporal trend claims descriptive rather than inferential.

Evidence assessment

Graded across the dimensions that decide whether you should act, each from what the source actually supports. There is no single score, and where a dimension was not assessed it says so.

Study design

moderate

Retrospective longitudinal genomic epidemiology; no intervention or comparator arm.

Directness

moderate

Describes resistance prevalence and trends in invasive Salmonella; clinically relevant but no patient outcomes reported.

Consistency

limited

Single global dataset; acknowledged inadequate surveillance in Africa and South America limits generalizability.

Risk of bias

limited

Retrospective analysis of aggregated national and public datasets; inherent heterogeneity and potential reporting bias not quantified.

Sample adequacy

strong

7,691 isolates across 77 countries over 70 years; large sample size supports prevalence estimates.

Source abstract

Abstract Antimicrobial resistance (AMR) in invasive Salmonella infections remains a global public health concern, and enhanced high-quality genomic surveillance is essential to inform guidelines and policies. Here, we aimed to describe clinically key antibiotic resistance trends in invasive Salmonella infections using 7691 isolates derived from national surveillance and publicly available datasets between 1954 and 2024. 29 (37.7%) of 77 countries identified at least one isolate with resistance or decreased susceptibility to ciprofloxacin, 25 (32.5%) and 29 (37.7%) countries resistance or decreased susceptibility to ceftriaxone and cefixime, 8 (10.4%) countries resistance to azithromycin, 15 (19.5%) countries resistance to fosfomycin, 10 (13.0%) countries resistance to colistin. Overall, 7.39% of 7691 isolates were resistant or decreased susceptibility to ciprofloxacin, 7.91% reported resistance or decreased susceptibility to 3GCs, 4.23% reported resistance to fosfomycin, and 0.79% reported resistance to azithromycin. Globally, azithromycin resistance is increasing, as is resistance or decreased susceptibility to ciprofloxacin, 3GCs, and 4GCs. However, surveillance levels remain inadequate in African and South American regions. We generated a global map of clinically key antibiotic resistance genes in invasive Salmonella infections worldwide. This retrospective, global, longitudinal genomic epidemiology study on invasive Salmonella provides evidence-based data for clinical guidelines, genomic surveillance, AMR control, and public health policies.

Follow from this

Taken from the source record, never inferred. Follow any of these and new work involving them reaches your briefing.

Yanan WangWufuer. XiayidanZiru YangYuhang PeiXiaolu PangMeilian Huang