Genetic source tracking of human plague cases in Inner Mongolia-Beijing, 2019

Abstract

On 12 November 2019, one couple from the Sonid Left Qi (County) in the Inner Mongolia Autonomous Region was diagnosed with pneumonic plague in Beijing. The wife acquired the infection from her husband. Thereafter, two bubonic plague cases were identified in Inner Mongolia on November 16th and 24th. In this study, genome-wide single nucleotide polymorphism (SNP) analysis was used to identify the phylogenetic relationship of Yersinia pestis strains isolated in Inner Mongolia. Strains isolated from reservoirs in 2018 and 2019 in Inner Mongolia, together with the strain isolated from Patient C, were further clustered into 2.MED3m, and two novel lineages (2.MED3q, 2.MED3r) in the 2.MED3 population. According to the analysis of PCR-based molecular subtyping methods, such as the MLVA 14 scheme and seven SNP allele sequencing, Patients A/B and D were classified as 2.MED3m. In addition, strains from rodents living near the patients’ residences were clustered into the same lineage as patients. Such observations indicated that human plague cases originated from local reservoirs. Corresponding phylogenetic analysis also indicated that rodent plague strains in different areas in Inner Mongolia belong to different epizootics rather than being caused by spreading from the same epizootic in Meriones unguiculatus in 2019.

Human Plague Case Diagnosed in Ningxia Tracked to Animal Reservoirs — Inner Mongolia Autonomous Region, China, 2021

“…Such results led the clinical doctors in GHNMU began to suspect the patient might suffer from plague and reported to the Ningxia CDC on August 20. This human plague case was confirmed via polymerase chain reaction (PCR) positive results in lymph node aspirates and blood by the Ningxia CDC within four hours, targeting the caf1, pla, and YPO0392 genes of Y. pestis (1), as well as the positive results of the colloidal gold-immunochromatography assay and reverse indirect hemagglutination assay (RIHA) test targeting the F1 antigen in lymph node aspirates and blood. The titer of RIHA for the lymph node aspirates and blood were 1∶64 and 1∶128, respectively.…”

“…In this event, the biochemical analyzer in GHNMU reported that bacteria in the patient's blood were of the Yersinia genus, even though it did not definitively that the sample was Y. pestis (due to lacking a corresponding database of bacteria), the clinicians began to suspect that the patient might have plague. It was the second time that such situation had occurred in China as the first occurred in Yunnan Province in 2016 (1). In fact, with the gains in technical competence in hospitals, there are many techniques such as the genome sequencing, biochemical analyzers, and massspectrometric techniques, that can firstly give the clinicians the clues to plague.…”

Retrospective analysis of dissemination of the 2.MED1 phylogenetic branch of Yersinia pestis in the Caucasus

“…This had a positive effect on the ecosystem of natural plague foci of the Caspian region. Against this background, strains of the medieval biovar caused multiple outbreaks of plague in the North-Western and Northern Caspian Sea regions, as well as outbreaks and isolated cases of plague in Central and East Asia in the 20th and 21st centuries [ 18 , 19 ].…”

Yersinia pestis and Plague: Some Knowns and Unknowns

“…Another potential dispersal method for the deliberate release of Y. pestis would be through a suicide attacker that would lead to an explosion in cases of pneumonic plague originating from a single source or multiple sources with secondary infections. Without adequate precautions modern transportation systems could then readily deliver plague rapidly across the globe [266].…”