Dataset Information

Complete Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Environmental Isolate from Zanzibar, Tanzania, Harboring Novel Insertion Elements and Two bla_CTX-M-15 Genes.

ABSTRACT: Here, we report the annotated whole-genome sequence of Klebsiella pneumoniae strain KP_3b, isolated in Zanzibar, Tanzania, from plastic litter. The strain is extended-spectrum β-lactamase (ESBL) producing and multidrug resistant, encoding 17 resistance genes, most of which are located on a 230,544-bp plasmid. The isolate contains two copies of the bla_CTX-M-15 gene and novel insertion elements.

SUBMITTER: Lallement C

PROVIDER: S-EPMC9387273 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

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Complete Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Environmental Isolate from Zanzibar, Tanzania, Harboring Novel Insertion Elements and Two blaCTX-M-15 Genes.

Lallement Claire C Krogfelt Karen A KA Skovgaard Ole O Jelsbak Lotte L

Microbiology resource announcements 20220714 8

Here, we report the annotated whole-genome sequence of Klebsiella pneumoniae strain KP_3b, isolated in Zanzibar, Tanzania, from plastic litter. The strain is extended-spectrum β-lactamase (ESBL) producing and multidrug resistant, encoding 17 resistance genes, most of which are located on a 230,544-bp plasmid. The isolate contains two copies of the blaCTX-M-15 gene and novel insertion elements. ...[more]

PMID: 35862907

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Project description:Escherichia coli sequence type 131 (ST131) has contributed to the spread of extended-spectrum beta-lactamase (ESBL) and has emerged as the dominant cause of hospital- and community-acquired urinary tract infections. Here, we report for the first time an in-depth analysis of whole-genome sequencing (WGS) of 4 ESBL-producing E. coli ST131 isolates recovered from patients in two hospitals in Armenia using Illumina short-read sequencing for accurate base calling to determine their genotype and to infer their phylogeny and using Oxford Nanopore Technologies long-read sequencing to resolve plasmid and chromosomal genetic elements. Genotypically, the four Armenian isolates were identified as part of the H30Rx/clade C2 (n = 2) and H41/clade A (n = 2) lineages and were phylogenetically closely related to isolates from the European Nucleotide Archive (ENA) database previously recovered from patients in the United States, Australia, and New Zealand. The Armenian isolates recovered in this study had chromosomal integration of the blaCTX-M-15 gene in the H30Rx isolates and a high number of virulence genes found in the H41 isolates associated with the carriage of a rare genomic island (in the context of E. coli ST131) containing the S fimbrial, salmochelin siderophore, and microcin H47 virulence genes. Furthermore, our data show the evolution of the IncF[2:A2:B20] plasmid harboring both blaCTX-M-15 and blaCTX-M-27 genes, derived from the recombination of genes from an IncF[F2:A-:B-] blaCTX-M-15-associated plasmid into the IncF[F1:A2:B20] blaCTX-M-27-associated plasmid backbone seen in two genetically closely related H41 Armenian isolates. IMPORTANCE Combining short and long reads from whole-genome sequencing analysis provided a genetic context for uncommon genes of clinical importance to better understand transmission and evolutionary features of ESBL-producing uropathogenic E. coli (UPEC) ST131 isolates recovered in Armenia. Using hybrid genome assembly in countries lacking genomic surveillance studies can inform us about new lineages not seen in other countries with genes encoding high virulence and antibiotic resistance harbored on mobile genetic elements.

Project description:BackgroundColistin is one of the few options for treating carbapenem-resistant Enterobacterales (CREs). There is little available information about the epidemic status of colistin-resistant CREs in Southern Sichuan, China. This study mainly investigated the genomic and phenotypic characteristics of an extensively drug resistant E. coli LZ00114 isolated from Luzhou, China.Materials and methodsIn 2020, LZ00114 was isolated from the urine of a patient with hydronephrosis and urinary tract infection in Luzhou, China. We assessed the resistance profile of LZ00114 in the presence and absence of the protonophore carbonyl cyano-m-chlorophenylhydrazine (CCCP) and 1-(1-naphthylmethyl)-piperazine (NMP) by antimicrobial susceptibility testing. The growth kinetics, motility, and pathogenicity of LZ00114 were determined to evaluate its microbial characteristics. In combination with whole genome sequencing (WGS) and real-time reverse transcription PCR (RT-PCR), we comprehensively analyzed the resistance mechanisms of LZ00114.ResultsLZ00114 was resistant to various antimicrobial agents, including meropenem, tetracycline, ciprofloxacin, gentamicin, fosfomycin, and polymyxin B. Notably, CCCP reversed the resistance of LZ00114 to polymyxin B. LZ00114 displayed high pathogenicity in the infection model (P<0.01) compared with the Lab-WT strain, and its growth rate and motility were not significantly different from the Lab-WT strain. WGS and conjugation revealed that LZ00114 belonged to ST410 and carried a bla NDM-5-harboring self-transmissible IncX3 plasmid and a multi-replicon IncFII/FIA/FIB plasmid carrying bla OXA-1-bla CTX-M-55-tet(B)-aac(6')-Ib-cr-dfrA17-sul1-fosA3. Comparative genomics revealed genetic relatedness between LZ00114 and strains isolated from other regions. Furthermore, there were point mutations in pmrA (S29G, G144S), pmrB (D283G, Y358N), marR (G103S, Y137H), emrA (I219V), and emrD (G323D) of LZ00114. RT-PCR confirmed the overexpression of efflux pumps and PmrABC in LZ00114.ConclusionThis study provides valuable information for the surveillance of antimicrobial resistance and a theoretical basis for the prevention and control of colistin-resistant E. coli. There is still a need to be vigilant about the clone spread of the high-risk clone group E. coli ST410.

Dataset Information

Complete Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Environmental Isolate from Zanzibar, Tanzania, Harboring Novel Insertion Elements and Two bla_CTX-M-15 Genes.

Publications

Complete Genome Sequence of a Multidrug-Resistant Klebsiella pneumoniae Environmental Isolate from Zanzibar, Tanzania, Harboring Novel Insertion Elements and Two <i>bla</i><sub>CTX-M-15</sub> Genes.

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