AUTHOR=Yuan Chao , Wei Yi , Zhang Si , Cheng Juan , Cheng Xiaolei , Qian Chengqian , Wang Yuhui , Zhang Yang , Yin Zhiqiu , Chen Hong 

TITLE=Comparative Genomic Analysis Reveals Genetic Mechanisms of the Variety of Pathogenicity, Antibiotic Resistance, and Environmental Adaptation of Providencia Genus

JOURNAL=Frontiers in Microbiology

VOLUME=11

YEAR=2020

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.572642

DOI=10.3389/fmicb.2020.572642

ISSN=1664-302X

ABSTRACT=<p>The bacterial genus <italic>Providencia</italic> is Gram-negative opportunistic pathogens, which have been isolated from a variety of environments and organisms, ranging from humans to animals. <italic>Providencia alcalifaciens</italic>, <italic>Providencia rettgeri</italic>, and <italic>Providencia stuartii</italic> are the most common clinical isolates, however, these three species differ in their pathogenicity, antibiotic resistance and environmental adaptation. Genomes of 91 isolates of the genus <italic>Providencia</italic> were investigated to clarify their genetic diversity, focusing on virulence factors, antibiotic resistance genes, and environmental adaptation genes. Our study revealed an open pan-genome for the genus <italic>Providencia</italic> containing 14,720 gene families. Species of the genus <italic>Providencia</italic> exhibited different functional constraints, with the core genes, accessory genes, and unique genes. A maximum-likelihood phylogeny reconstructed with concatenated single-copy core genes classified all <italic>Providencia</italic> isolates into 11 distant groups. Comprehensive and systematic comparative genomic analyses revealed that specific distributions of virulence genes, which were highly homologous to virulence genes of the genus <italic>Proteus</italic>, contributed to diversity in pathogenicity of <italic>Providencia alcalifaciens</italic>, <italic>Providencia rettgeri</italic>, and <italic>Providencia stuartii</italic>. Furthermore, multidrug resistance (MDR) phenotypes of isolates of <italic>Providencia rettgeri</italic> and <italic>Providencia stuartii</italic> were predominantly due to resistance genes from class 1 and 2 integrons. In addition, <italic>Providencia rettgeri</italic> and <italic>Providencia stuartii</italic> harbored more genes related to material transport and energy metabolism, which conferred a stronger ability to adapt to diverse environments. Overall, our study provided valuable insights into the genetic diversity and functional features of the genus <italic>Providencia</italic>, and revealed genetic mechanisms underlying diversity in pathogenicity, antibiotic resistance and environmental adaptation of members of this genus.</p>