A core genome approach that enables prospective and dynamic monitoring of infectious outbreaks

Aggelen, Helen van; Kolde, Raivo; Chamarthi, Hareesh; Loving, Joshua; Fan, Yu; Fallon, John T.; Huang, Weihua; Wang, Guiqing; Fortunato-Habib, Mary M.; Carmona, Juan J.; Gross, Brian D.

doi:10.1038/s41598-019-44189-0

Cited by 7 publications

(3 citation statements)

References 39 publications

(34 reference statements)

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“…The finalized cgMLST Oxford scheme represents thus 82% of the reference genome NCTC11168, which places this typing scheme as an intermediate between a core genome and a whole genome MLST scheme with a total of 1,343 loci vs. 637/678 for the two others. A sample-set independent approach was recently proposed to select a conserved-sequence genome as a novel core genome methodology to address this issue ( Van Aggelen et al., 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes

Nennig

Llarena

Herold

et al. 2021

Front. Cell. Infect. Microbiol.

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Campylobacter jejuni is the leading cause of bacterial gastroenteritis, which has motivated the monitoring of genetic profiles circulating in Luxembourg since 13 years. From our integrated surveillance using a genotyping strategy based on an extended MLST scheme including gyrA and porA markers, an unexpected endemic pattern was discovered in the temporal distribution of genotypes. We aimed to test the hypothesis of stable lineages occurrence by implementing whole genome sequencing (WGS) associated with comprehensive and internationally validated schemes. This pilot study assessed four WGS-based typing schemes to classify a panel of 108 strains previously identified as recurrent or sporadic profiles using this in-house typing system. The strain collection included four common lineages in human infection (N = 67) initially identified from recurrent combination of ST-gyrA-porA alleles also detected in non-human samples: veterinary (N = 19), food (N = 20), and environmental (N = 2) sources. An additional set of 19 strains belonging to sporadic profiles completed the tested panel. All the strains were processed by WGS by using Illumina technologies and by applying stringent criteria for filtering sequencing data; we ensure robustness in our genomic comparison. Four typing schemes were applied to classify the strains: (i) the cgMLST SeqSphere+ scheme of 637 loci, (ii) the cgMLST Oxford scheme of 1,343 loci, (iii) the cgMLST INNUENDO scheme of 678 loci, and (iv) the wgMLST INNUENDO scheme of 2,795 loci. A high concordance between the typing schemes was determined by comparing the calculated adjusted Wallace coefficients. After quality control and analyses with these four typing schemes, 60 strains were confirmed as members of the four recurrent lineages regardless of the method used (N = 32, 12, 7, and 9, respectively). Our results indicate that, regardless of the typing scheme used, epidemic or endemic signals were detected as reflected by lineage B (ST2254-gyrA9-porA1) in 2014 or lineage A (ST19-gyrA8-porA7), respectively. These findings support the clonal expansion of stable genomes in Campylobacter population exhibiting a multi-host profile and accounting for the majority of clinical strains isolated over a decade. Such recurring genotypes suggest persistence in reservoirs, sources or environment, emphasizing the need to investigate their survival strategy in greater depth.

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Section: Discussionmentioning

confidence: 99%

Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes

Nennig

Llarena

Herold

et al. 2021

Front. Cell. Infect. Microbiol.

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“…For further analysis, the annotation was performed using PROKKA v1.11 [ 34 ], and only the genome sequences with >20× depth coverage were considered. We considered 20× to be the minimum coverage to include the maximum number of our isolates ( n = 90 out of a total n = 109) for core genome analysis, variant determination, and monitoring of infectious outbreaks in other previous studies [ 35 , 36 , 37 ]. Plasmids were predicted and reconstructed from the assembled genomes using MOB-suite [ 38 ] and classified as conjugative, mobilisable, and non-mobilisable plasmids.…”

Section: Methodsmentioning

confidence: 99%

WGS-Based Lineage and Antimicrobial Resistance Pattern of Salmonella Typhimurium Isolated during 2000–2017 in Peru

et al. 2022

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Salmonella Typhimurium is associated with foodborne diseases worldwide, including in Peru, and its emerging antibiotic resistance (AMR) is now a global public health problem. Therefore, country-specific monitoring of the AMR emergence is vital to control this pathogen, and in these aspects, whole genome sequence (WGS)—based approaches are better than gene-based analyses. Here, we performed the antimicrobial susceptibility test for ten widely used antibiotics and WGS-based various analyses of 90 S. Typhimurium isolates (human, animal, and environment) from 14 cities of Peru isolated from 2000 to 2017 to understand the lineage and antimicrobial resistance pattern of this pathogen in Peru. Our results suggest that the Peruvian isolates are of Typhimurium serovar and predominantly belong to sequence type ST19. Genomic diversity analyses indicate an open pan-genome, and at least ten lineages are circulating in Peru. A total of 48.8% and 31.0% of isolates are phenotypically and genotypically resistant to at least one antibiotic, while 12.0% are multi-drug resistant (MDR). Genotype–phenotype correlations for ten tested drugs show >80% accuracy, and >90% specificity. Sensitivity above 90% was only achieved for ciprofloxacin and ceftazidime. Two lineages exhibit the majority of the MDR isolates. A total of 63 different AMR genes are detected, of which 30 are found in 17 different plasmids. Transmissible plasmids such as lncI-gamma/k, IncI1-I(Alpha), Col(pHAD28), IncFIB, IncHI2, and lncI2 that carry AMR genes associated with third-generation antibiotics are also identified. Finally, three new non-synonymous single nucleotide variations (SNVs) for nalidixic acid and eight new SNVs for nitrofurantoin resistance are predicted using genome-wide association studies, comparative genomics, and functional annotation. Our analysis provides for the first time the WGS-based details of the circulating S. Typhimurium lineages and their antimicrobial resistance pattern in Peru.

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“…The advantage of using the species core genome is that the length of alignments remains constant regardless of the number and diversity of strains being compared, making SNP distances directly comparable. 6,7 The main limitation is that a significant portion of the genome (ie, the accessory genome) is ignored in comparisons, limiting the resolution that can be achieved.…”

mentioning

confidence: 99%

Key variables affecting genetic distance calculations in genomic epidemiology

Coll

2021

The Lancet Microbe

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Key variables affecting genetic distance calculations in genomic epidemiologyThe benefits of using whole-genome sequencing for outbreak detection and surveillance of bacterial pathogens have been well documented in recent years. 1,2 However, the bioinformatics methods used to analyse and interpret genomic data need to be standardised and validated if genomic epidemiology is to be widely implemented and routinely used in public health investigations. This means that genome analysis methods should yield robust, reproducible and generalisable results regardless of the geographical origin, laboratory, or bacterial population of study.Key to transmission inference is the determination and interpretation of genetic distances from bacterial genomic data. The simplest way to establish genetic relatedness between bacterial isolates is to count the number of nucleotide differences (ie, the number of single-nucleotide polymorphisms [SNPs]) between their genome sequences. Genetic relatedness thresholds have been proposed above which recent bacterial transmission can be ruled out, while distances below Lancet Microbe 2021

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A core genome approach that enables prospective and dynamic monitoring of infectious outbreaks

Cited by 7 publications

References 39 publications

Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes

Investigating Major Recurring Campylobacter jejuni Lineages in Luxembourg Using Four Core or Whole Genome Sequencing Typing Schemes

WGS-Based Lineage and Antimicrobial Resistance Pattern of Salmonella Typhimurium Isolated during 2000–2017 in Peru

Key variables affecting genetic distance calculations in genomic epidemiology

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