Threshold-free genomic cluster detection to track transmission pathways in health-care settings: a genomic epidemiology analysis

Hawken, Shawn E.; Yelin, Rachel D; Lolans, Karen; Pirani, Ali; Weinstein, Robert A.; Lin, Michael; Hayden, Mary K; Snitkin, Evan S.

doi:10.1016/s2666-5247(22)00115-x

Cited by 4 publications

(4 citation statements)

References 31 publications

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“…We tested a range of SNP thresholds to minimize the bias possibly introduced by a single cutoff. The minimum SNP threshold was set to be 14 SNPs based on the mutation rate of our collection and the reference genome length (see methods), and the maximum was defined to be 25 SNPs based on recent regional epidemiologic studies 7 , 16 – 18 .…”

Section: Resultsmentioning

confidence: 99%

“…Of greater concern, using an SNP-based transmission tracking method, we revealed that the prevalence of O2v1:KL64-hvKP was driven by an altered transmission pattern. The accuracy of SNP-based transmission tracking methods has been recently evidenced by numerous studies using large datasets for various pathogens, like MRSA and CRKP 7 , 16 , 40 . In particular, we here used a range of SNP cutoffs to avoid any bias that could be caused by a single cutoff.…”

Section: Discussionmentioning

confidence: 99%

“…A range of thresholds was used here to identify recent intra- and inter-facility transmission pairs using pairwise distances. The minimum threshold was determined as 14 SNPs (2 × 5,716,474 × 1.2256 × 10 −6 ) using reference genome length (5,716,474 base pairs) and mutation rate (1.2256 × 10 −6 mutations per base pair per year estimated in this study), and the maximum threshold was defined as 25 SNPs according to recent studies of CRKP transmission 7 , 16 – 18 . This analysis was performed using the regentrans package 72 in R v4.1.1.…”

Section: Methodsmentioning

confidence: 99%

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A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China

Zhou¹,

Xue²,

Xu³

et al. 2023

Nat Commun

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Adaptation to selective pressures is crucial for clinically important pathogens to establish epidemics, but the underlying evolutionary drivers remain poorly understood. The current epidemic of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant threat to public health. In this study we analyzed the genome sequences of 794 CRKP bloodstream isolates collected in 40 hospitals in China between 2014 and 2019. We uncovered a subclonal replacement in the predominant clone ST11, where the previously prevalent subclone OL101:KL47 was replaced by O2v1:KL64 over time in a stepwise manner. O2v1:KL64 carried a higher load of mobile genetic elements, and a point mutation exclusively detected in the recC of O2v1:KL64 significantly promotes recombination proficiency. The epidemic success of O2v1:KL64 was further associated with a hypervirulent sublineage with enhanced resistance to phagocytosis, sulfamethoxazole-trimethoprim, and tetracycline. The phenotypic alterations were linked to the overrepresentation of hypervirulence determinants and antibiotic genes conferred by the acquisition of an rmpA-positive pLVPK-like virulence plasmid and an IncFII-type multidrug-resistant plasmid, respectively. The dissemination of the sublineage was further promoted by more frequent inter-hospital transmission. The results collectively demonstrate that the expansion of O2v1:KL64 is correlated to a repertoire of genomic alterations convergent in a subpopulation with evolutionary advantages.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China

Zhou¹,

Xue²,

Xu³

et al. 2023

Nat Commun

View full text Add to dashboard Cite

show abstract

“…StrainPhlAn characterizes two genomes as representing different strains if >0.1 % of nucleotides in species-specific marker sequences are polymorphic [50]. However, as an example, in a genomic epidemiologic study of Klebsiella pneumoniae , SNV thresholds were misleading, with significant false-positive and false-negative transmission inferences [51]. Alternatively, an ANI threshold (or a variation on the standard ANI measure) is often used to make such a distinction, although a range of values have been used [44, 52, 53].…”

Section: Discussionmentioning

confidence: 99%

Evidence of Lactobacillus strains shared between the female urinary and vaginal microbiota

Atkins,

Sabharwal,

Boger

et al. 2024

Microbial Genomics

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Lactobacillus species are common inhabitants of the ‘healthy’ female urinary and vaginal communities, often associated with a lack of symptoms in both anatomical sites. Given identification by prior studies of similar bacterial species in both communities, it has been hypothesized that the two microbiotas are in fact connected. Here, we carried out whole-genome sequencing of 49 Lactobacillus strains, including 16 paired urogenital samples from the same participant. These strains represent five different Lactobacillus species: L. crispatus, L. gasseri, L. iners, L. jensenii, and L. paragasseri. Average nucleotide identity (ANI), alignment, single-nucleotide polymorphism (SNP), and CRISPR comparisons between strains from the same participant were performed. We conducted simulations of genome assemblies and ANI comparisons and present a statistical method to distinguish between unrelated, related, and identical strains. We found that 50 % of the paired samples have identical strains, evidence that the urinary and vaginal communities are connected. Additionally, we found evidence of strains sharing a common ancestor. These results establish that microbial sharing between the urinary tract and vagina is not limited to uropathogens. Knowledge that these two anatomical sites can share lactobacilli in females can inform future clinical approaches.

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Diversity and persistence of MRSA and VRE in skilled nursing facilities: environmental screening, whole-genome sequencing and development of a dispersion index

Cassone¹,

Wang²,

Lansing³

et al. 2023

Journal of Hospital Infection

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Threshold-free genomic cluster detection to track transmission pathways in health-care settings: a genomic epidemiology analysis

Cited by 4 publications

References 31 publications

A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China

A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China

Evidence of Lactobacillus strains shared between the female urinary and vaginal microbiota

Diversity and persistence of MRSA and VRE in skilled nursing facilities: environmental screening, whole-genome sequencing and development of a dispersion index

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