Streptococcus pseudopneumoniae: Use of Whole-Genome Sequences To Validate Species Identification Methods

Jensen, Christian Salgård; Iversen, Katrine Højholt; Dargis, Rimtas; Shewmaker, Patricia L.; Rasmussen, Simon; Christensen, Jens Jørgen; Nielsen, Xiaohui Chen

doi:10.1128/jcm.02503-20

Cited by 6 publications

(3 citation statements)

References 35 publications

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“…cgMLST, core-genome SNP analysis, and ANI schemes demonstrated their ability to subtype species with the same MLST denominations ( 28 , 31 , 41 ). ANI with more than 95% identity was considered suitable to identify species and ≥98% to identify subspecies ( 29 – 31 ). In this study, the comparison of K. quasipneumoniae subsp.…”

Section: Discussionmentioning

confidence: 99%

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Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes

Altayb

Hosawi²,

Baothman³

et al. 2023

Front. Public Health

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IntroductionThe emergence of bacterial pathogens in environmental hosts represents a major risk to public health. This study aimed at characterizing seven novel environmental strains of K. quasipneumoniae using a genomic approach which was misidentified by phenotypic methods in a previous batch of 27 species thought to be K. pneumoniae.MethodsWhole-genome sequencing was performed using the Illumina platform, and the generated raw reads were de novo assembled. Comparative genomic, resistome, virulome, mobilome, and phylogeny were then investigated using dierent bioinformatics tools.ResultsSix strains were identified as K. quasipneumoniae subsp similipneumoniae and one as K. quasipneumoniae subsp. quasipneumoniae. All isolates were resistant to ampicillin, cephalexin, and amoxicillin-clavulanic acid and harbored the fosA, blaOKP types, oqxB, and oqxA genes. One isolate additionally harbored a gene cassettes consisting of blaSHV−1, blaOXA−1, aac(6′)-Ib-cr, catB genes. The aminoglycoside-modifying enzyme gene aph(3”)-Ia was bracketed by two insertion elements. Plasmid analyses showed that IncFIBK was the most prevalent plasmid, circulating in six isolates, while one isolate exhibited seven different plasmids. The isolates have virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (iutA), salmochelins (iroE, iroN), enterobactin siderophore, adherence, and biofilm formation (mrkA, mrkB, mrkC, mrkD, mrkF, and mrkH).ConclusionOur study highlights the ecology and transmission of K. quasipneumoniae (which have the ability to disseminate to other environmental sources including animals) outside the clinical setting and the contribution of water, vegetables, and table surfaces as potential reservoirs of farm-to-fork transmission of disease via local markets in Khartoum, Sudan.

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Section: Discussionmentioning

confidence: 99%

“…Heat map and SNP matrix were built by FastANI_heatmap using R code for building a heat map and histogram with the output of FastANI. ANI with more than 95% identity was considered suitable to identify species and ≥ 98% to identify subspecies ( 29 – 31 ).…”

Section: Methodsmentioning

confidence: 99%

Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes

Altayb

Hosawi²,

Baothman³

et al. 2023

Front. Public Health

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show abstract

“…Isolates from the ODiD-project were sequenced using the Illumina NextSeq 500 platform and pair-end sequencing and The Center for Genomic Epidemiology pipeline (Rebelo et al, 2022). Species identification was confirmed by cgMLSA from WGS data (Jensen et al, 2021). Software Pathogenwatch (Wellcome Sanger Institute) 2 was used for MLST and molecular serotyping of S. pneumoniae isolates.…”

Section: Wgs Species Identification Multi Locus Sequence Typing (Mlst...mentioning

confidence: 99%

Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci

Eriksen

Fuursted²,

Jensen³

et al. 2023

Front. Microbiol.

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IntroductionFor Streptococcus pneumoniae, β-lactam susceptibility can be predicted from the amino acid sequence of the penicillin-binding proteins PBP1a, PBP2b, and PBP2x. The combination of PBP-subtypes provides a PBP-profile, which correlates to a phenotypic minimal inhibitory concentration (MIC). The non-S. pneumoniae Mitis-group streptococci (MGS) have similar PBPs and exchange pbp-alleles with S. pneumoniae. We studied whether a simple BLAST analysis could be used to predict phenotypic susceptibility in Danish S. pneumoniae isolates and in internationally collected MGS.MethodIsolates with available WGS and phenotypic susceptibility data were included. For each isolate, the best matching PBP-profile was identified by BLAST analysis. The corresponding MICs for penicillin and ceftriaxone was retrieved. Category agreement (CA), minor-, major-, and very major discrepancy was calculated. Genotypic-phenotypic accuracy was examined with Deming regression.ResultsAmong 88 S. pneumoniae isolates, 55 isolates had a recognized PBP-profile, and CA was 100% for penicillin and 98.2% for ceftriaxone. In 33 S. pneumoniae isolates with a new PBP-profile, CA was 90.9% (penicillin) and 93.8% (ceftriaxone) using the nearest recognized PBP-profile. Applying the S. pneumoniae database to non-S. pneumoniae MGS revealed that none had a recognized PBP-profile. For Streptococcus pseudopneumoniae, CA was 100% for penicillin and ceftriaxone in 19 susceptible isolates. In 33 Streptococcus mitis isolates, CA was 75.8% (penicillin) and 86.2% (ceftriaxone) and in 25 Streptococcus oralis isolates CA was 8% (penicillin) and 100% (ceftriaxone).ConclusionUsing a simple BLAST analysis, genotypic susceptibility prediction was accurate in Danish S. pneumoniae isolates, particularly in isolates with recognized PBP-profiles. Susceptibility was poorly predicted in other MGS using the current database.

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Identification of Streptococcus pseudopneumoniae and other mitis group streptococci using matrix assisted laser desorption/ionization - time of flight mass spectrometry

Jensen

Dargis

Shewmaker

et al. 2021

Diagnostic Microbiology and Infectious Disease

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Streptococcus pseudopneumoniae: Use of Whole-Genome Sequences To Validate Species Identification Methods

Cited by 6 publications

References 35 publications

Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes

Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes

Predicting β-lactam susceptibility from the genome of Streptococcus pneumoniae and other mitis group streptococci

Identification of Streptococcus pseudopneumoniae and other mitis group streptococci using matrix assisted laser desorption/ionization - time of flight mass spectrometry

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