Complete Genome Sequence of Kluyvera intestini sp. nov., Isolated from the Stomach of a Patient with Gastric Cancer

et al. 2020

BMC Genomics

Background: Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a strain of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient with a biliary tract infection. We explored the biological and genomic characteristics of this strain to provide new evidence and detailed information for opportunistic pathogens about the co-infection they may cause.Results: The isolate grew very slowly but conferred strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumoniae. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. Like its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both the natural environment and animal host, over 30 mobile genetic elements, and a plasmid bearing bla CTX-M-3 gene, indicating its ability to disseminate antimicrobial-resistant genes from the natural environment to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18, which could serve as targets for novel antimicrobial strategies. Conclusions: Our findings imply that AF18 and its species are not only infection-relevant but also potential disseminators of antibiotic resistance genes, which highlights the need for continuous monitoring for this novel species and efforts to develop treatment strategies.

Section: Discussionmentioning

confidence: 99%

“…MRY16-398 carries bla IMP-6 , bla CTX-M-2 , and aadA2 gene [23], and the [Kluyvera] intestini str. GT-16 contains many ARGs that even confer resistance to polymyxin [25]. A more distant relative of AF18-Pytobacter ursingii (previously named Kluyvera intermedia) was found to be KPC positive and carbapenem-resistant [28].…”

Section: Discussionmentioning

confidence: 99%

Genomic characterization of an emerging Enterobacteriaceae species: the first case of co-infection with a typical pathogen in a human patient

Zhao

et al. 2020

BMC Genomics

“…Except AF18 which cause a co-infection with a typical pathogen, two of the other strains of this species ( [Kluyvera] intestini str. GT-16 [46], and Matakosakonia sp.MRY16_398 [44]) were both isolated from patients in Japan, while the other three strains (Enterobacter sp.NFR05, Enterobacter sp.Bisph2, and Enterobacteriaceae bacterium ENNIH2) were isolated from rhizoplane (China), sandy soil (Algeria) [47], and hospital sewage (USA) [45], respectively, indicating a wide range of environments that this species can inhabit.…”

Section: Discussionmentioning

confidence: 99%

“…MRY16-398 carries bla IMP-6 , bla CTX-M-2 , and aadA2 gene [44], and the [Kluyvera] intestini str. GT-16 contains many ARGs that even confer resistance to polymyxin [46]. A more distant relative of AF18-Pytobacter ursingii (previously named Kluyvera intermedia) was found to be KPC positive and carbapenem-resistant [49].…”

Section: Annotation Of Genes In the Genome Supports That Af18 Possessmentioning

confidence: 99%

Genomic Characterization of an Emerging Enterobacteriaceae Species: the First Case of Co-infection With a Typical Pathogen in a Human Patient

Zhang

et al. 2020

Preprint

Background: Opportunistic pathogens are important for clinical practice as they often cause antibiotic-resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a strain of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient with a biliary tract infection. We explored the biological and genomic characteristics of this strain to provide new evidence and detailed information for opportunistic pathogens about the co-infection they may cause.Results: The isolate grew very slowly but conferred strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumoniae. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. Like its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both the natural environment and animal host, over 30 mobile genetic elements, and a plasmid bearing blaCTX-M-3 gene, indicating its ability to disseminate antimicrobial-resistant genes from the natural environment to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18, which could serve as targets for novel antimicrobial strategies. Conclusions: Our findings imply that AF18 and its species are not only infection-relevant but also potential disseminators of antibiotic resistance genes, which highlights the need for continuous monitoring for this novel species and efforts to develop treatment strategies.

“…pathogen, two of the other strains of this species( [Kluyvera] intestini str. GT-16(Tetz et al, 2017), and Matakosakonia sp.MRY16_398 (Sekizuka et al, 2018)) were both isolated from patients in Japan, while the other three strains (Enterobacter sp.NFR05, Enterobacter sp.Bisph2, and Enterobacteriaceae bacterium ENNIH2) were isolated from rhizoplane (China), sandy soil (Algeria)(Benslama and Boulahrouf, 2016), and hospital sewage (USA)(Weingarten et al, 2018), respectively, indicating a wide range of environments the species inhabits.Annotation of genes in the genome supports that AF18 possesses many common features of Enterobacteriaceae family, such as the flagella that confer mobility to the bacterium, many genetic mobile elements that facilitate transfer of stress-adaptive genes, especially those of ARGs. In fact, strains of the species have been found an important source of extended-spectrum β-lactamase-encoding genes and even carbapenem-resistant genes.…”

mentioning

confidence: 99%

Genomic Characterization of an Emerging Enterobacteriaceae Species for the First Case of Human Infection in Cooperation with a Typical Pathogen

Zhang

et al. 2020

Preprint

Opportunistic pathogens are important for clinical practice as they often cause antibiotic resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a novel species of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient of biliary tract infection. The isolate grows very slowly but confers strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumonia. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis, and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains respectively isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. As its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both wild environment and animal host, tens of genetic mobile elements, and a plasmid bearing blaCTX-M-3 gene, indicating its ability to disseminate antimicrobial resistant genes from wild to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18 which could serve as targets for novel antimicrobial strategies. These findings imply that AF18 and its species are not only infection-relevant but also potential disseminators in transferring antibiotic determinants, which highlights the need for continuous monitoring for this novel species and efforts to develop controlling strategies.