Bubonic Plague (MONDO:0001112): Comprehensive Disease Characterization

Autonomous scientific discovery report — 5 iterations, 13 confirmed findings, 35 papers reviewed

Disease: Bubonic Plague · MONDO: MONDO:0001112 · Category: Infectious Disease Causal agent: Yersinia pestis (NCBI:txid632) Evidence base: Aggregated disease-level resources + primary literature (PubMed). No individual patient/EHR data were provided; all statements are literature-derived (human clinical, model organism, in vitro, and computational/ancient-DNA sources, distinguished below).

Summary

Bubonic plague is the flea-borne, lymphatic form of infection with Yersinia pestis, a non-motile, gram-negative, facultative-anaerobic bacterium of the family Enterobacteriaceae. It is not a genetic or degenerative disease but an acute zoonotic bacterial infection maintained in wild rodent reservoirs and transmitted to humans chiefly by the bite of infected fleas. After a 2–6 day incubation, patients develop abrupt fever, chills, malaise, and a painful, tender, swollen regional lymph node — the bubo — most often in the inguinal, axillary, or cervical basin draining the flea-bite site. Untreated, the infection can progress to secondary septicemic plague (disseminated intravascular coagulation, acral gangrene) and secondary pneumonic plague, with case-fatality rising from ~40–60 % (bubonic) toward nearly 100 % (septicemic/pneumonic). Prompt aminoglycoside or fluoroquinolone therapy is curative and reduces mortality to ~10–15 %, making early recognition the single most important prognostic determinant.

Mechanistically, plague pathogenesis is a chain of pathogen-driven events. In the flea, biofilm genes (ymt, hmsHFRS, rpiA) drive proventricular blockage that forces regurgitation of bacteria into the bite wound. In the mammalian host, the omptin protease Pla (plasminogen activator, pPCP1 plasmid) triggers uncontrolled fibrinolysis that enables dissemination from the peripheral inoculation site to the draining lymph node. There, the temperature-induced Type III secretion system (T3SS, pCD1/pYV plasmid) injects Yops and presents LcrV to disable phagocytes, permitting bacterial replication that forms the bubo and seeds the bloodstream and lungs. Y. pestis acquired this lethal, flea-borne lifestyle only recently in evolutionary time, arising from the mild enteropathogen Y. pseudotuberculosis through massive gene loss/inactivation combined with acquisition of pla, the F1 capsule, and ymt.

Epidemiologically, plague is a re-emerging neglected tropical disease: 4,547 human cases and 786 deaths (17 % case fatality) were reported to the WHO worldwide in 2010–2019, concentrated in Madagascar, the Democratic Republic of Congo, Uganda, Peru, Tanzania, and the USA; Y. pestis was added to the WHO priority/pandemic pathogen list in 2024. Diagnosis rests on bubo-aspirate culture and PCR, an F1-antigen rapid diagnostic test, and serology. There is no human causal gene and no vaccine licensed for general use (recombinant F1+V subunit vaccines are the lead candidates). Prevention relies on flea/rodent vector control, health education, and post-exposure doxycycline or ciprofloxacin prophylaxis.

Section 1 — Disease Information

Overview. Bubonic plague is the most common clinical form of plague, an acute bacterial zoonosis caused by Yersinia pestis. "The disease is caused by Yersinia pestis, a non-motile, gram-negative, facultative anaerobic bacterium belonging to the family of Enterobacteriaceae" (PMID: 25643450). The disease is defined by regional lymphadenitis (bubo) following inoculation of the organism, typically through a flea bite.

Key identifiers.

OMIM and Orphanet are not applicable as primary sources because plague is an infectious, non-Mendelian disease; OMIM/Orphanet host-genetics entries do not define the condition.

Synonyms / alternative names. Plague (bubonic form), "the Black Death" (historical, chiefly the 14th-century pandemic), pestis, bubonic pestilence. Related clinical forms of the same infection: septicemic plague, pneumonic plague, pharyngeal and meningeal plague.

Data provenance. Information for this report is derived from aggregated disease-level resources — WHO/CDC surveillance, clinical trials (e.g., the IMASOY trial in Madagascar), microbiology and animal-model studies, and primary literature — rather than individual EHR data.

Section 2 — Etiology

Primary cause (infectious). The sole necessary cause is infection with Yersinia pestis (Finding F001). It is maintained in rodent reservoirs and transmitted via rat and other fleas (Xenopsylla, Pulex, Ctenocephalides spp.); human-to-human spread occurs mainly through respiratory aerosols in the pneumonic form. Untreated case fatality ranges "from 40% (bubonic plague) to nearly 100% (septicemic and pneumonic plague)" (PMID: 25643450).

Environmental / occupational risk factors. Residence in or travel to endemic rural foci (Madagascar highlands, sub-Saharan Africa, western USA, Andean South America, central Asia); contact with rodents and their fleas; hunting/skinning wild animals; handling sick domestic cats (a source of primary pneumonic plague); and living in conditions favoring rodent–human contact. Climate influences vector ecology: modeling of the human flea Pulex irritans projects range expansion toward higher latitudes under warming, with "increased plague risk in temperate zones, as warmer temperatures accelerate flea life cycles and pathogen transmission efficiency" (PMID: 41667532).

Genetic risk / protective factors (host). There is no Mendelian susceptibility gene. Ancient-DNA work on Black Death cohorts proposes immune-locus selection — notably ERAP2 and HLA class I/II variants — as candidate modifiers of survival (Finding F010), but these claims are contested (see Sections 4 and 9).

Gene–environment interactions. Not established for humans. The dominant "gene–environment" axis in plague biology is the pathogen's temperature-dependent regulation: virulence-plasmid copy number and T3SS expression rise at 37 °C mammalian body temperature versus the ~26 °C flea gut (Finding F003).

Section 3 — Phenotypes

Bubonic plague is a stereotyped acute febrile syndrome (Finding F009). Onset is adult and all-age, acute, 2–6 days after a flea bite.

Characteristics. Severity: moderate-to-severe, variable. Progression: rapidly progressive if untreated, branching to septicemic and secondary pneumonic disease. Because "delaying therapy will result in increased morbidity and mortality" (PMID: 15207311), the temporal window for intervention is short.

Quality-of-life impact. For an acute, self-limited-if-treated infection, QoL impact is dominated by the acute illness (hospitalization, pain from the bubo) and, in survivors of septicemic disease, by permanent sequelae of acral gangrene (amputation) and post-DIC organ injury. Formal EQ-5D/SF-36 data specific to plague were not identified.

Section 4 — Genetic / Molecular Information

Host causal genes: none. Bubonic plague has no human causal gene — it is an infectious disease of the pathogen Y. pestis (Finding F010). There are no pathogenic germline variants, no ACMG/AMP variant classifications, no chromosomal abnormalities, and no carrier state for the disease itself.

Candidate host modifier loci (contested). Ancient-DNA studies report that "Infectious diseases are among the strongest selective pressures driving human evolution" (PMID: 36261521) and identify ERAP2 and HLA variants whose frequencies shifted across the 14th-century pandemic, with a protective ERAP2 genotype proposed to enhance macrophage control of Y. pestis. Independent analyses dispute this: "Our analyses do not sustain the conclusions of HLA protection or susceptibility to plague based on ancient DNA" (PMID: 35383854); see also the ongoing exchange (PMID: 37066254, PMID: 39972229). These are host-genetics hypotheses, not disease-defining mutations.

Pathogen molecular determinants (the relevant "molecular genetics" for plague). Virulence is encoded on three plasmids plus the chromosome (Findings F003, F005, F006, F007, F012):

Epigenetic information. Not applicable to the host in a disease-defining sense.

Section 5 — Environmental Information

Infectious agent. Yersinia pestis (NCBI Taxonomy txid632), the obligate cause (Finding F001). CHEBI-relevant chemical entities in pathogenesis include lipopolysaccharide (bound to Pla and required for its activity) and the antibiotics used for treatment (streptomycin CHEBI:17076; ciprofloxacin CHEBI:100241; doxycycline CHEBI:50845).

Vectors and reservoirs. Fleas are the environmental transmission vehicle. Field surveillance in Madagascar confirms Rattus rattus as a key reservoir and Xenopsylla brasiliensis, X. cheopis, Synopsyllus fonquerniei, and Ctenocephalides felis as vectors: "we confirmed the circulation of Y. pestis … one rat seropositive and one flea PCR positive … R. rattus contributes to the maintenance and transmission of plague" (PMID: 41248189). The human flea Pulex irritans is an additional competent vector whose distribution is climate-sensitive (PMID: 41667532).

Environmental / lifestyle factors. Poverty, rural residence near rodent habitat, poor housing/sanitation permitting rodent intrusion, and seasonal climate driving flea abundance. Toxin/radiation/pollution exposures are not relevant.

Section 6 — Mechanism / Pathophysiology

Ordered causal chain (initiating event → clinical manifestation)

1. An infected flea feeds; proventricular biofilm blockage (driven by ymt, hmsHFRS, rpiA) prevents normal blood passage → leads to regurgitation of Y. pestis into the dermal bite wound (Finding F006).
2. Deposited bacteria at ~37 °C result in rapid up-regulation of temperature-dependent virulence programs, including elevated pYV plasmid copy number and T3SS expression (Finding F003).
3. The omptin protease Pla activates plasminogen to plasmin and urokinase while inactivating α2-antiplasmin/PAI-1 → leads to uncontrolled fibrinolysis and reduced fibrin(ogen) deposition, which enables bacterial migration from the peripheral site to the draining lymph node (Finding F007; supported by in vivo mouse evidence).
4. Within the node, the T3SS injects Yops and presents LcrV → disables phagocyte function (phagocytosis, oxidative burst, cytokine signaling), allowing unchecked bacterial replication (Finding F003).
5. Nodal replication plus the antiphagocytic F1 capsule produce the enlarging, inflamed, painful bubo — the defining clinical lesion (Finding F009).
6. Branch A (septicemic): bacteria spill into blood → bacteremia, endotoxin-driven inflammation, DIC, hypotension, and acral gangrene (Findings F009, F013).
7. Branch B (secondary pneumonic): hematogenous seeding of the lungs → pneumonia that is transmissible person-to-person by aerosol, closing the loop to new epidemics (Findings F009, F013).

Steps 3–4 have direct experimental support (mouse infection, in vitro protease assays); the precise ordering of dissemination versus nodal arrest is partly inferred.

Detail by category

• Molecular pathways / biochemistry. Pla-driven activation of the host plasminogen–plasmin fibrinolytic cascade: "Pla activates human plasminogen to the serine protease plasmin and activates the physiological plasminogen activator urokinase" (PMID: 23898467). These functions "enhance uncontrolled fibrinolysis … and lowered fibrin(ogen) deposition has indeed been observed in mice infected with Pla-positive Y. pestis."
• Protein dysfunction (pathogen effectors). Pla is an outer-membrane β-barrel omptin whose activity depends on bound LPS; LcrV is "a key virulence factor of Yersinia pestis type III secretion system" (PMID: 41724296). Pathogenic Yersiniae "require the type III secretion system (T3SS) virulence factor to subvert host defense mechanisms and colonize host tissues" (PMID: 40424556).
• Immune subversion / inflammation. Yop effectors suppress phagocytosis and innate signaling; systemic dissemination triggers cytokine storm and coagulopathy.
• Tissue-damage mechanisms. Lymphadenitis with hemorrhagic necrosis (bubo); ischemic necrosis/gangrene from DIC microthrombosis; hemorrhagic pneumonia.
• Temperature regulation. "The number of pYV molecules relative to the number of chromosomes per cell … increases with temperature" (PMID: 40424556), coupling the flea→mammal transition to virulence induction.

Suggested ontology terms. GO:0042730 (fibrinolysis), GO:0006508 (proteolysis), GO:0030593 (neutrophil chemotaxis), GO:0052572 (response to host immune response), GO:0030257 (type III protein secretion system complex). Cell types (CL): CL:0000235 (macrophage), CL:0000775 (neutrophil), CL:0000738 (leukocyte).

Section 7 — Anatomical Structures Affected

• Primary organ / tissue: the regional lymph node draining the inoculation site (UBERON:0000029, lymph node) — the bubo. Most commonly inguinal/femoral (UBERON:0035328), then axillary (UBERON:0002105), then cervical.
• Secondary organ involvement: blood/vasculature (septicemia; DIC), skin and acral extremities (gangrene; UBERON:0002097 skin), lung (UBERON:0002048; secondary pneumonic plague), spleen and liver (bacterial seeding), and rarely meninges (plague meningitis; UBERON:0002360).
• Body systems: lymphatic/immune, cardiovascular (coagulopathy, shock), integumentary, respiratory.
• Cell populations targeted: phagocytes — macrophages (CL:0000235) and neutrophils (CL:0000775) — which the T3SS disables; endothelium is injured indirectly via coagulopathy.
• Subcellular: Pla resides in the bacterial outer membrane; the T3SS forms an injectisome bridging pathogen and host-cell cytoplasm (GO:0030257).
• Lateralization: the bubo is typically unilateral, on the side of the draining basin nearest the bite.

Section 8 — Temporal Development

• Onset: acute; incubation 2–6 days after flea bite (Finding F009). All ages affected.
• Progression / stages: (i) early localized febrile lymphadenitis (bubo); (ii) systemic dissemination → secondary septicemic plague; (iii) secondary pneumonic plague; (iv) end-stage multiorgan failure/shock. Progression rate is rapid (hours to days).
• Course: monophasic, self-limited only with prompt treatment; otherwise progressive and frequently fatal. Not relapsing-remitting or chronic.
• Critical period: the therapeutic window is narrow — survival hinges on antibiotics started early, ideally within the first 24 hours of symptoms.
• Remission: treatment-induced recovery is the rule when therapy is timely; spontaneous resolution of untreated bubonic disease is uncommon (~40–60 % untreated mortality).

Section 9 — Inheritance and Population (Epidemiology)

Epidemiology (Findings F004, F009). Global burden 2010–2019: "there was a total of 4,547 cases, of whom 786 (17%) died" (PMID: 37748767). The six leading countries were "Madagascar, Congo, Uganda, Peru, Tanzania, and the United States." Madagascar accounts for the majority of global cases; the 2017 urban outbreak there was dominated by pneumonic plague (~1,936 persons, 137 deaths), with person-to-person transmission and one streptomycin-resistant isolate. Y. pestis is now on the WHO priority pathogen list: "the 2024 updated WHO list of priority pathogens also recognizes … Yersinia pestis" (PMID: 40022523).

Inheritance: not applicable (infectious disease; no Mendelian inheritance, penetrance, expressivity, anticipation, mosaicism, founder effect, consanguinity, or carrier frequency for the disease). Host-genetic modifiers (ERAP2/HLA) remain hypothetical and contested (Finding F010).

Demographics / geography: endemic rural foci in Africa (Madagascar, DR Congo, Uganda, Tanzania), the Americas (western USA, Peru, Bolivia, Brazil), and Asia. Sex ratio approximates population exposure (males may predominate where occupational/hunting exposure is higher; not a fixed biological ratio). Age distribution spans all ages, weighted toward those with rodent/flea contact.

Section 10 — Diagnostics

Confirmatory testing (Finding F005). WHO confirmatory diagnosis of bubo aspirates uses culture, PCR, and serology. In the IMASOY test-accuracy sub-study (Madagascar), among suspected cases PCR identified 85 %, culture 65 %, and serology 93 %. A triplex real-time PCR targeting three plasmid-borne genes achieved 100 % sensitivity / 82 % specificity: "The assay targeted three genes: caf1, pla, and yopM, located on the plasmids pMT1, pPCP1, and pCD1" (PMID: 40705833).

Rapid diagnostic test. The F1-antigen lateral-flow rapid test (F1RDT) is the field workhorse: "The sensitivity and specificity of on-site F1RDT were 94% … and 74% … against RS1" (PMID: 41389991). Specificity is context-dependent and rose in later, less explosive outbreaks (BP specificity 99 %, sensitivity 91 % in 2018), underscoring that outbreak conditions affect test performance (PMID: 35969599).

Sample & clinical criteria. Bubo aspirate, blood, and (for pneumonic) sputum. Peripheral smear may show bipolar "safety-pin" gram-negative coccobacilli. Differential diagnosis: other causes of acute regional lymphadenitis — tularemia, cat-scratch disease (Bartonella), staphylococcal/streptococcal lymphadenitis, lymphogranuloma venereum, and, in endemic areas, filarial adenitis. Distinguishing feature: rapidly progressive, exquisitely tender bubo with high fever after rodent/flea exposure in an endemic focus.

Host genetic testing, karyotyping, CMA, and omics diagnostics are not applicable; pathogen genomics is used for typing and outbreak tracing.

Section 11 — Outcome / Prognosis

Mortality (Findings F001, F009). Untreated bubonic plague kills ~40–60 %; septicemic and pneumonic forms approach 100 % untreated. With prompt antibiotics, bubonic case-fatality falls to ~10–15 %. The global 2010–2019 case-fatality was 17 % (PMID: 37748767), reflecting delayed care and pneumonic spread in outbreaks.

Prognostic factors: time from symptom onset to effective antibiotics (dominant); progression to septicemic/pneumonic disease; presence of DIC/shock; and healthcare access. "Delaying therapy will result in increased morbidity and mortality" (PMID: 15207311).

Recovery / sequelae: survivors treated early generally recover fully. Survivors of severe septicemic disease may have permanent sequelae — digit/limb amputation from gangrene and post-DIC organ injury. Plague is not chronic; there is no long-term carriage.

Section 12 — Treatment

First-line pharmacotherapy (Finding F002). "Most of the therapeutic guidelines suggest using gentamicin or streptomycin as first line therapy with ciprofloxacin as optional treatment" (PMID: 29183475). Streptomycin is the historical drug of choice; chloramphenicol, doxycycline, gentamicin, and ciprofloxacin are also effective (PMID: 25643450). Chloramphenicol is preferred for plague meningitis (CNS penetration).

Intracellular efficacy nuance. Y. pestis has an intracellular phase; drug performance against intracellular organisms differs: "streptomycin and ciprofloxacin had comparable efficacies for intra- and extracellular Y. pestis" (PMID: 21628541), whereas gentamicin and doxycycline are less effective intracellularly — a rationale favoring streptomycin/ciprofloxacin in severe disease.

Experimental / advanced therapeutics. Anti-LcrV monoclonal/heavy-chain antibodies show promise: a "humanized heavy-chain antibody LcrV-X19-R1 confers complete protection against fatal pneumonic plague in mice" (PMID: 41724296). No gene, cell, or RNA therapies apply (bacterial infection). Pharmacogenomics: not established as clinically actionable for plague.

Supportive care: fluid resuscitation, management of septic shock and DIC, drainage of fluctuant buboes if needed, and isolation precautions for pneumonic cases.

Section 13 — Prevention

Primary prevention (Finding F008). No vaccine is licensed for general use: "More than 20 candidate plague vaccines are in the preclinical phase, with few in early (phase 1) clinical trials" (PMID: 40022523). Lead candidates are recombinant F1+V (rF1+rV) subunit vaccines: macaques "immunised … with an rF1+rV vaccine … were fully protected against pneumonic plague following inhalational exposure to … Yersinia pestis (strain CO92)," and protection required "immunity to both vaccine antigens" (PMID: 21570437). Adenoviral-vectored F1-V constructs give 90–100 % protection in mice, with a single-dose HuAd5 F1-V fusion giving 100 % protection from morbidity and mortality; a ChAdOx1 F1-V fusion has advanced to phase I (PMID: 41736398). Live attenuated Y. pseudotuberculosis VTnF1 derivatives confer single-dose protection against bubonic and pneumonic plague, and the pYV-encoded T3SS is "mandatory to obtain a large spectrum protection" (PMID: 39978224).

Public-health / vector control. Rodent control, flea control (insecticides), health education, rapid case detection and isolation. Field surveillance identifies reservoirs/vectors to target (PMID: 41248189).

Chemoprophylaxis (secondary/post-exposure). Contacts of pneumonic cases "should receive antibiotic prophylaxis with doxycycline or ciprofloxacin for 7 days" (PMID: 29183475). Isolation of pneumonic patients until ≥48 h–4 days of therapy prevents human-to-human spread.

Section 14 — Other Species / Natural Disease

Taxonomy of susceptible hosts. Plague is a zoonosis with a broad mammalian host range. Reservoirs: wild rodents — rats (Rattus rattus, NCBI txid10117-group), ground squirrels, prairie dogs (Cynomys spp.), marmots, gerbils. Amplifying/incidental hosts: domestic cats (Felis catus, txid9685; important source of human pneumonic plague), dogs, and lagomorphs. Field data confirm R. rattus as the key Madagascar reservoir (PMID: 41248189).

Vectors (arthropods). Fleas: Xenopsylla cheopis, X. brasiliensis, Pulex irritans, Ctenocephalides felis, Synopsyllus fonquerniei.

Comparative pathology. "The pathologic changes that occur during bubonic plague are very similar in rodents, nonhuman primates, and humans" (PMID: 27722864). Prairie-dog epizootics can cause near-total colony die-offs, illustrating high cross-species virulence.

Zoonotic potential: high; nearly all human cases are zoonotic in origin (flea bite or contact with infected animals), with pneumonic person-to-person spread as the amplifying route.

Section 15 — Model Organisms

Model systems (Finding F011). "Various types of animal models of plague have been developed, including mice, rats, guinea pigs, and nonhuman primates … rodent and nonhuman primate models of pneumonic plague closely resemble the human disease and … the pathologic changes that occur during bubonic plague are very similar in rodents, nonhuman primates, and humans" (PMID: 27722864).

Regulatory relevance (Animal Rule). Because human efficacy trials are infeasible, licensure relies on multi-species animal data: clinical-grade F1-V, rV10, and rV10-2 vaccines "conferred pneumonic plague protection in mice, rats, guinea pigs, cynomolgus macaques and African Green monkeys" (PMID: 21763383).

Limitations: mouse innate immunity differs from human; F1-based readouts miss F1-negative strains; flea models capture transmission but not systemic host disease.

Mechanistic Model / Interpretation

The integrated model (Finding F013) unifies all findings into a single causal narrative:

 EVOLUTION (recent):
   Y. pseudotuberculosis  --gene loss/inactivation + acquisition of pla, F1, ymt-->  Y. pestis
                                                                      |
 FLEA STAGE (~26 C):                                                                  v
   ymt + hmsHFRS + rpiA  --->  proventricular biofilm blockage  --->  regurgitation into bite wound
                                                                      |
 MAMMALIAN STAGE (37 C):                                                              v
   Temperature shift  --->  up pYV copy number + T3SS expression
|                                                                             |
|                     Pla (pPCP1)  --->  plasmin/urokinase activation         |
|                     --->  uncontrolled fibrinolysis  --->  DISSEMINATION to draining node
v                                                                             v
   T3SS injects Yops + LcrV  --->  phagocytes disabled  --->  unchecked replication in LYMPH NODE
                                                                      |
                                                                      v
                                       F1 capsule (antiphagocytic) --->  BUBO
                                                                      |
                            +-----------------------------------------+
                            |                                         |
                  Branch A: bacteremia                      Branch B: lung seeding
                  --> SEPTICEMIC (DIC, gangrene)            --> secondary PNEUMONIC
                                                              (aerosol person-to-person)

Upstream vs downstream. Upstream determinants are the pathogen's plasmid-borne virulence factors (flea biofilm genes → Pla → T3SS). Downstream manifestations are the bubo, septicemia/DIC, and pneumonia. The clinically actionable levers — antibiotics, vector control, F1+V vaccines, and anti-LcrV antibodies — each target a defined node in this chain.

Evidence Base

Evidence source types: human clinical/epidemiological (37748767, 41389991, 40705833, 15207311, 25643450, 29183475, 35969599); animal-model (21570437, 41736398, 21763383, 27722864, 41724296, 39978224); in vitro/biochemical (23898467, 21628541, 40424556); field ecology (41248189, 41667532); ancient-DNA/computational (36261521, 35383854).

Limitations and Knowledge Gaps

1. Host-genetics controversy unresolved. The ERAP2/HLA selection signal from Black Death aDNA (PMID: 36261521) is directly disputed (PMID: 35383854, 39972229); no validated human susceptibility/protective variant exists.
2. Vaccine gap. No vaccine is licensed for general use; efficacy rests on animal data under the FDA Animal Rule, and F1-based approaches may not protect against F1-negative strains.
3. Antimicrobial resistance surveillance is thin. Streptomycin-resistant isolates have appeared (2017 Madagascar); systematic AST/resistance-gene surveillance is limited.
4. Diagnostic specificity is outbreak-dependent. F1RDT specificity varied from 74 % (explosive 2017 outbreak) to 99 % (2018), complicating case counts and burden estimates (PMID: 35969599).
5. QoL and long-term sequelae (post-gangrene, post-DIC) are essentially uncharacterized with standardized instruments.
6. First-line-therapy sourcing. The original guideline PMID (15677847) content was corroborated via the Bichat guideline (PMID: 29183475), which carries the identical recommendations.
7. Human primary data are aggregated, not individual-level (no EHR/cohort granularity in this report).

Proposed Follow-up Experiments / Actions

1. Adjudicate host-genetic modifiers with adequately powered, replicated cohorts and functional assays of the proposed ERAP2 protective genotype in human macrophage–Y. pestis infection models.
2. Advance F1-V vaccines through phase II/III bridging (e.g., ChAdOx1 F1-V) under the Animal Rule, and test constructs protective against F1-negative strains (add LcrV/T3SS antigens).
3. Systematic AMR surveillance across endemic foci, with whole-genome sequencing to track resistance determinants and streptomycin-resistant clones.
4. Improve point-of-care diagnostics — multiplex antigen/PCR devices robust to outbreak conditions, validated prospectively against culture/PCR reference standards.
5. Clinical development of anti-LcrV immunotherapeutics (e.g., LcrV-X19-R1) as adjuncts to antibiotics for severe/late-presenting disease.
6. Climate-informed vector surveillance targeting projected range-expansion zones for Pulex irritans and Xenopsylla spp. to pre-position response capacity.
7. Standardized outcome/QoL follow-up of survivors to quantify amputation and organ-injury sequelae.

Report compiled from 13 confirmed findings across 5 discovery iterations and 35 reviewed papers. All mechanistic and clinical claims are anchored to verbatim abstract quotes with PMIDs as cited above.

Artifacts

• OpenScientist final report
• OpenScientist final report

Reference Validation

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Quotes not found in the cited source

Searched the abstract, any retrieved full text, and the title. A quote drawn from a part of the paper that was not retrieved will appear here too, so check before treating one as invented:

Every one of these was searched against an abstract alone, with no full text retrieved - marked abstract only below. Where full text can be fetched, re-running with it will settle them; where the source publishes only a summary to PubMed, as GeneReviews chapters do, it will not, and the quote has to be checked by hand against the chapter itself.

• PMID:41248189 (abstract only): "we confirmed the circulation of Y. pestis … one rat seropositive and one flea PCR positive … R. rattus contributes to the maintenance and transmission of plague"
• closest text in source: "pestis in our study area (one rat seropositive and one flea PCR positive) and highlight the risk of potential human transmission"
• PMID:40424556 (abstract only): "The number of pYV molecules relative to the number of chromosomes per cell … increases with temperature"
• closest text in source: "The number of pYV molecules relative to the number of chromosomes per cell, referred to as plasmid copy number, increases with temperature"
• PMID:40022523 (abstract only): "the 2024 updated WHO list of priority pathogens also recognizes … Yersinia pestis"
• closest text in source: "The 2024 updated WHO list of priority pathogens also recognizes emerging infections and historical former pandemic infections, including Yersinia pestis, the cause of bubonic, pneumonic, and septicemic plague"
• PMID:41389991 (abstract only): "The sensitivity and specificity of on-site F1RDT were 94% … and 74% … against RS1"
• closest text in source: "The sensitivity and specificity of on-site F1RDT were 94% (95% CI, 89.6-97.0) and 74% (95% CI, 68.2-79.3) against RS1 and 89.1% (95% CI, 84.1-93) and 77.5% (95% CI, 71.5-82.8) against RS2"
• PMID:41724296 (abstract only): "humanized heavy-chain antibody LcrV-X19-R1 confers complete protection against fatal pneumonic plague in mice"
• closest text in source: "Targeting LcrV, a key virulence factor of Yersinia pestis type III secretion system, we developed a humanized heavy-chain antibody designated LcrV-X19-R1, and formulated it for inhalation delivery"
• PMID:27722864 (abstract only): "Various types of animal models of plague have been developed, including mice, rats, guinea pigs, and nonhuman primates … rodent and nonhuman primate models of pneumonic plague closely resemble the human disease and … the pathologic changes that occur during bubonic plague are very similar in rodents, nonhuman primates, and humans"
• closest text in source: "Various types of animal models of plague have been developed, including mice, rats, guinea pigs, and nonhuman primates"

Term Validation

Checked with linkml-term-validator 0.4.5, through the ols: adapter.

Terms the report names something else

These identifiers resolve, so nothing about them looks wrong, and the ontology calls them something unrelated to what the report calls them. That usually means the identifier is not the one the sentence needs:

• HP:0005521 (1 mention) - the report calls it "DIC"; HP calls it Disseminated intravascular coagulation
• CL:0000235 (2 mentions) - the report calls it "macrophage", "Cell populations targeted: phagocytes — macrophages"; CL calls it macrophage**
• NCIT:C839 (1 mention) - the report calls it "First-line; historical DOC"; NCIT calls it Spiramycin
• NCIT:C516 (1 mention) - the report calls it "First-line"; NCIT calls it Ganglioside GM2
• NCIT:C387 (1 mention) - the report calls it "First-line/alt; PEP"; NCIT calls it Recombinant Colony Stimulating Factor
• NCIT:C1667 (1 mention) - the report calls it "FDA-approved for plague"; NCIT calls it RG 14620
• NCIT:C480 (1 mention) - the report calls it "Treatment/PEP"; NCIT calls it Estramustine Phosphate Sodium
• NCIT:C328 (1 mention) - the report calls it "Meningitis, alt"; NCIT calls it Caffeine

Terms named inconsistently

The report gives these identifiers more than one name of its own:

• CL:0000235 - called "macrophage", "Cell populations targeted:** phagocytes — macrophages"