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Studies show that those cases infected by carbapenem-resistant pathogens have a higher morbidity and mortality rate compared with those who are infected by non-carbapenem-resistant pathogens (Cai et al., 2017; Duin, Kaye, Neuner, & Bonomo, 2013). Therefore, early discerning of the CP genes and their resistance mechanisms are considered crucial to aid in infection control as well as lessen the likelihood of mortality, duration of hospitalization stay, and related medical costs (Duin et al., 2013; Nordmann & Poirel, 2019). Further, it is understood that the cocarriage of genes encoding different classes of carbapenemases could confer higher resistance to carbapenem antibiotics, which may promote further spread of the disease (Wang et al., 2019).

CPgeneProfiler: A lightweight R package to profile the Carbapenamase genes from genome assemblies