Growth, biofilm formation, and motility of Listeria monocytogenes strains isolated from food and clinical samples located in Shanghai (China)

Listeria monocytogenes is a common foodborne pathogen that frequently causes global outbreaks. In this study, the growth characteristics, biofilm formation ability, motility ability and whole genome of 26 L. monocytogenes strains isolated from food and clinical samples in Shanghai (China) from 2020 to 2022 were analyzed. There are significant differences among isolates in terms of growth, biofilm formation, motility, and gene expression. Compared with other sequence type (ST) types, ST1930 type exhibited a significantly higher maximum growth rate, the ST8 type demonstrated a stronger biofilm formation ability, and the ST121 type displayed greater motility ability. Furthermore, ST121 exhibited significantly high mRNA expression levels compared with other ST types in virulence genes mpl, fbpA and fbpB, the quorum sensing gene luxS, starvation response regulation gene relA, and biofilm adhesion related gene bapL. Whole-genome sequencing (WGS) analyses indicated the isolates of lineage I were mostly derived from clinical, and the isolates of lineage II were mostly derived from food. The motility ability, along with the expression of genes associated with motility (motA and motB), exhibited a significantly higher level in lineage II compared with lineage I. The isolates from food exhibited significantly higher motility ability compared with isolates from clinical. By integrating growth, biofilm formation, motility phenotype with molecular and genotyping information, it is possible to enhance comprehension of the association between genes associated with these characteristics in L. monocytogenes.

Rapid detection of plasmid-mediated AmpC-producers by eazyplex® SuperBug AmpC assay compared to whole-genome sequencing

Current methods for plasmid-mediated AmpC β-lactamase (pAmpC) detection in routine microbiological laboratories are based on various phenotypic tests. Eazyplex®SuperBug AmpC assay is a molecular assay based on isothermal amplification for rapid detection of the most common pAmpC types from bacterial culture: CMY-2 group, DHA, ACC and MOX. Our aim was to evaluate the diagnostic performance of this assay. The assay was evaluated on 64 clinical isolates of Enterobacterales without chromosomal inducible AmpC, and with phenotypically confirmed AmpC production. The results were confirmed, and isolates further characterized by whole-genome sequencing (WGS). eazyplex®SuperBug AmpC assay correctly detected the two most common pAmpC types CMY-2 group (16/16) and DHA (19/19). Detection of ACC and MOX could not be evaluated on our set of isolates since there was only one isolate harbouring ACC and none with MOX. pAmpC encoding genes could be detected in only eight of 36 investigated Escherichia coli isolates. The remaining 28 E. coli isolates harboured previously described mutations in the blaEC promoter, leading to the overexpression of chromosomally encoded E. coli specific AmpC β-lactamase. All results were 100% concordant with the results of WGS. eazyplex®SuperBug AmpC assay enabled rapid and reliable detection of pAmpC-encoding genes in Enterobacterales like Klebsiella spp. and Proteus spp. and the distinction between plasmid-mediated and chromosomally encoded AmpC in E. coli.

Raw milk cheeses from Beira Baixa, Portugal-A contributive study for the microbiological hygiene and safety assessment

Due to specific bacterial microbiota, raw milk cheeses have appreciated sensory properties. However, they may pose a threat to consumer safety due to potential pathogens presence. This study evaluated the microbiological contamination of 98 raw milk cheeses from Beira Baixa, Portugal. Presence and enumeration of Coagulase Positive Staphylococci (CPS), Listeria monocytogenes, Salmonella spp., pathogenic Escherichia coli, and indicator microorganisms (non-pathogenic E. coli and Listeria spp.) was attained. E. coli antimicrobial resistance (AMR) was also evaluated. PCR and/or Whole genome sequencing (WGS) was used to characterize E. coli, Salmonella spp. and L. monocytogenes isolates. Sixteen cheeses (16.3%) were classified as Satisfactory, 59 (60.2%) as Borderline and 23 (23.5%) as Unsatisfactory/Potential Injurious to Health. L. monocytogenes, CPS > 104 cfu g-1, Extraintestinal pathogenic E. coli (ExPEC) and Salmonella spp. were detected in 4.1%, 6.1%, 3.1% and 1.0% of the samples, respectively. Listeria innocua (4.1%) and E. coli > 104 cfu g-1 (16.3%) were also detected. AMR E. coli was detected in 23/98 (23.5%) of the cheese samples, of which two were multidrug resistant. WGS identified genotypes already associated to human disease and Listeria spp. cluster analysis indicated that cheese contamination might be related with noncompliance with Good Hygiene Practices during cheese production.

Assessing the discriminability of PCR-based open reading frame typing versus single-nucleotide polymorphism analysis via draft whole-genome sequencing of methicillin-resistant Staphylococcus aureus in nosocomial transmission analysis

Phylogenetic analysis based on single-nucleotide polymorphism (SNP)-based through whole-genome sequencing is recognized as the standard method for probing nosocomial transmission. However, the application of WGS is constrained by the high cost of equipment and the need for diverse analysis tools, which limits its widespread use in clinical laboratory settings. In Japan, the prevalent use of PCR-based open reading frame typing (POT) for tracing methicillin-resistant Staphylococcus aureus (MRSA) transmission routes is attributed to its simplicity and ease of use. Although POT's discriminatory power is considered insufficient for nosocomial transmission analysis, conclusive data supporting this notion is lacking. This study assessed the discriminatory capabilities of SNP analysis and POT across 64 clinical MRSA strains. All 21 MRSA strains of ST5/SCCmec IIa, having more than 16 SNPs, demonstrated distinct clones. Conversely, two strains shared the same POT number and were identified as group A. Among the 12 MRSA strains of ST8/SCCmec IVl with over nine SNPs, five fell into POT group B, and five into POT group C. All four MRSA strains of ST8/SCCmec IVa were classified into POT group D, although they included strains with more than 30 SNPs. Among the 27 MRSA strains of ST1/SCCmec IVa, 14 were classified into POT group E. However, except for two clusters (each comprising two or three strains), all had SNP counts >10 (Fig.1-D). SNP analysis of MRSA in CC1/SCCmec IV showed that several strains had the same number of SNPs in POT number (106-183-37), even among bacteria with >100 SNPs, indicating POT's limited use in detailed nosocomial transmission analysis.

Comparative pangenomic analysis of Campylobacter fetus isolated from Spanish bulls and other mammalian species

Campylobacter fetus comprises two closely related mammal-associated subspecies: Campylobacter fetus subsp. fetus (Cff) and Campylobacter fetus subsp. venerealis (Cfv). The latter causes bovine genital campylobacteriosis, a sexually-transmitted disease endemic in Spain that results in significant economic losses in the cattle industry. Here, 33 C. fetus Spanish isolates were whole-genome sequenced and compared with 62 publicly available C. fetus genomes from other countries. Genome-based taxonomic identification revealed high concordance with in silico PCR, confirming Spanish isolates as Cff (n = 4), Cfv (n = 9) and Cfv biovar intermedius (Cfvi, n = 20). MLST analysis assigned the Spanish isolates to 6 STs, including three novel: ST-76 and ST-77 for Cfv and ST-78 for Cff. Core genome SNP phylogenetic analysis of the 95 genomes identified multiple clusters, revealing associations at subspecies and biovar level between genomes with the same ST and separating the Cfvi genomes from Spain and other countries. A genome-wide association study identified pqqL as a Cfv-specific gene and a potential candidate for more accurate identification methods. Functionality analysis revealed variations in the accessory genome of C. fetus subspecies and biovars that deserve further studies. These results provide valuable information about the regional variants of C. fetus present in Spain and the genetic diversity and predicted functionality of the different subspecies.

Inferring Mycobacterium Tuberculosis Drug Resistance and Transmission using Whole-genome Sequencing in a High TB-burden Setting in China

Objective

China is among the 30 countries with a high burden of tuberculosis (TB) worldwide, and TB remains a public health concern. Kashgar Prefecture in the southern Xinjiang Autonomous Region is considered as one of the highest TB burden regions in China. However, molecular epidemiological studies of Kashgar are lacking.

Methods

A population-based retrospective study was conducted using whole-genome sequencing (WGS) to determine the characteristics of drug resistance and the transmission patterns.

Results

A total of 1,668 isolates collected in 2020 were classified into lineages 2 (46.0%), 3 (27.5%), and 4 (26.5%). The drug resistance rates revealed by WGS showed that the top three drugs in terms of the resistance rate were isoniazid (7.4%, 124/1,668), streptomycin (6.0%, 100/1,668), and rifampicin (3.3%, 55/1,668). The rate of rifampicin resistance was 1.8% (23/1,290) in the new cases and 9.4% (32/340) in the previously treated cases. Known resistance mutations were detected more frequently in lineage 2 strains than in lineage 3 or 4 strains, respectively: 18.6% vs. 8.7 or 9%, P < 0.001. The estimated proportion of recent transmissions was 25.9% (432/1,668). Multivariate logistic analyses indicated that sex, age, occupation, lineage, and drug resistance were the risk factors for recent transmission. Despite the low rate of drug resistance, drug-resistant strains had a higher risk of recent transmission than the susceptible strains (adjusted odds ratio, 1.414; 95% CI, 1.023-1.954; P = 0.036). Among all patients with drug-resistant tuberculosis (DR-TB), 78.4% (171/218) were attributed to the transmission of DR-TB strains.

Conclusion

Our results suggest that drug-resistant strains are more transmissible than susceptible strains and that transmission is the major driving force of the current DR-TB epidemic in Kashgar.

Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing

The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics.

Invasive Streptococcus agalactiae (group B streptococcus) infection with toxic shock-like syndrome: A report of a fatal non-pregnant case and a review of the literature

Streptococcus agalactiae (group B streptococcus; GBS) is a Gram-positive coccus. It has emerged as a cause of significant infections in non-pregnant adults, particularly neonates and individuals aged 65 years or older, which can lead to fatal outcomes. Streptococcal toxic shock-like syndrome (STSS) is an acute illness, which is mainly caused by exotoxin-producing strains of Streptococcus pyogenes and may result in death. In this report, we present a fatal non-pregnant case of STSS induced by GBS in a 45-year-old healthy female. The patient presented with fever, polyarthralgia, myalgia, and skin erythema. Matrix Assisted Laser Desorption/Ionization‒Time of Flight Mass Spectrometry (MALDI-TOF-MS) and PCR identified GBS in colonies from her blood and urine cultures, and she was diagnosed with septicemia and STSS. On the sixth day of her illness, she died from acute respiratory distress syndrome and multiple organ dysfunction syndrome. Whole-genome sequencing revealed the presence of several virulence genes in the genome of the GBS strain detected in the blood cultures, which may have contributed to the development of STSS and the patient's death.

Whole genome sequencing and annotation of Scleroderma yunnanense, the only edible Scleroderma species

Scleroderma yunnanense, an ectomycorrhizal fungus, is a popular edible mushroom within the Yunnan Province of Southwest China that holds great ecological and economic implications. However, despite its significance, there remains limited information about this species. Therefore, we sequenced S. yunnanense genome to identify the functional genes of S. yunnanense involved in secondary metabolite and carbohydrate production pathways. First, we present the 40.43 Mb high-quality reference genome for S. yunnanense, distributed across 35 contigs; moreover, the N50 contig size was found to reach 3.31 Mb and contained 8877 functional genes. Finally, genome annotation was conducted to compare the functional genes of S. yunnanense with protein sequences from different publicly available databases. Taken together, we identified 12 biosynthetic gene clusters across 10 contigs; among these were 13 key mevalonate (MVA) pathway enzymes, a key tyrosinase enzyme in the 3,4-dihydroxyphenylalanine (DOPA) pathway that is responsible for producing DOPA melanins, and 16 enzymes involved in uridine diphosphate glucose biosynthesis. Overall, this study presents the first genome assembly and annotation of S. yunnanense; ultimately, this information will be important in the elucidation of the biological activities and artificial domestication of this fungus.

Power of NGS-based tests in HSP diagnosis: analysis of massively parallel sequencing in clinical practice

Hereditary spastic paraplegia (HSP) refers to a group of heterogeneous neurological disorders mainly characterized by corticospinal degeneration (pure forms), but sometimes associated with additional neurological and extrapyramidal features (complex HSP). The advent of next-generation sequencing (NGS) has led to huge improvements in knowledge of HSP genetics and made it possible to clarify the genetic etiology of hundreds of "cold cases," accelerating the process of reaching a molecular diagnosis. The different NGS-based strategies currently employed as first-tier approaches most commonly involve the use of targeted resequencing panels and exome sequencing, whereas genome sequencing remains a second-tier approach because of its high costs. The question of which approach is the best is still widely debated, and many factors affect the choice. Here, we aim to analyze the diagnostic power of different NGS techniques applied in HSP, by reviewing 38 selected studies in which different strategies were applied in different-sized cohorts of patients with genetically uncharacterized HSP.

Carbapenemase-producing Gram-negative bacteria in hospital wastewater, wastewater treatment plants and surface waters in a metropolitan area in Germany, 2020

Carbapenemase-producing bacteria (CPB) such as Klebsiella pneumoniae and Escherichia coli are causing hospital outbreaks worldwide. An important transfer route into the aquatic environment is the urban water cycle. We aimed to determine the presence of CPB in hospital wastewater, wastewater treatment plants (WWTPs) and surface waters in a German metropolitan area and to characterise these bacteria by whole-genome comparisons. During two periods in 2020, 366 samples were collected and cultivated on chromogenic screening media. Bacterial colonies were selected for species identification and PCR-based carbapenemase gene screening. Genomes of all detected CPB were sequenced and analysed for resistance gene content, followed by multilocus sequence typing (MLST) and core genome MLST (cgMLST) for K. pneumoniae and E. coli isolates. Carbapenemase genes were detected in 243 isolates, most of which belonged to genera/species Citrobacter spp. (n = 70), Klebsiella spp. (n = 57), Enterobacter spp. (n = 52) and E. coli (n = 42). Genes encoding KPC-2 carbapenemase were detected in 124 of 243 isolates. K. pneumoniae produced mainly KPC-2 and OXA-232 whereas E. coli harboured various enzymes (KPC-2, VIM-1, OXA-48, NDM-5, KPC-2 + OXA-232, GES-5, GES-5 + VIM-1, IMP-8 + OXA-48). Eight and twelve sequence types (STs) were identified for K. pneumoniae and E. coli, respectively, forming different clusters. The detection of numerous CPB species in hospital wastewater, WWTPs and river water is of concern. Genome data highlight a hospital-specific presence of distinct carbapenemase-producing K. pneumoniae and E. coli strains belonging to "global epidemic clones" in wastewater samples representing local epidemiology. The various detected CPB species including E. coli ST635, which is not known to cause human infections, could serve as reservoirs/vectors for the spread of carbapenemase genes in the environment. Therefore, effective pretreatment of hospital wastewater prior to discharge into the municipal wastewater system may be required, although swimming lakes do not appear to be a relevant risk factor for CPB ingestion and infection.

Establishment and genetically characterization of patient-derived xenograft models of cervical cancer

Purpose

Patient-derived xenograft (PDX) models were established to reproduce the clinical situation of original cancers and have increasingly been applied to preclinical cancer research. Our study was designed to establish and genetically characterize cervical cancer PDX models.

Methods

A total of 91 fresh fragments obtained from 22 surgically resected cervical cancer tissues were subcutaneously engrafted into female NOD-SCID mice. Hematoxylin and eosin (H&E) staining was performed to assess whether the established PDX models conserved the histological features of original patient cervical cancer tissues. Moreover, a Venn diagram was applied to display the overlap of all mutations detected in whole-genome sequencing (WGS) data from patient original cervical cancer (F0) and F2-, F3-PDX models. The whole exome sequencing (WES) and the “maftools” package were applied to determine the somatic mutations among primary cervical cancers and the established PDX models.

Results

Our study successfully developed a panel of cervical cancer PDX models and the latency time of cervical cancer PDX model establishment was variable with a progressive decrease as the passage number increased, with a mean time to initial growth of 94.71 days in F1 engraftment to 40.65 days in F3 engraftment. Moreover, the cervical cancer PDX models preserved the histological features of their original cervical cancer. WGS revealed that the genome of original cervical cancer was preserved with high fidelity in cervical cancer PDX models throughout the xenografting and passaging process. Furthermore, WES demonstrated that the cervical cancer PDX models maintained the majority somatic mutations of original cervical cancer, of which the KMT2D, LRP1B, NAV3, TP53, FAT1, MKI67 and PKHD1L1 genes were identified as the most frequently mutated genes.

Conclusions

The cervical cancer PDX models preserved the histologic and genetic characteristics of their original cervical cancer, which helped to gain a deeper insight into the genetic alterations and lay a foundation for further investigation of the molecular targeted therapy of cervical cancer.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01342-5.

Comparative whole-genome sequence analysis of a BoNT/B5-producing Clostridium botulinum isolate from an infant botulism case of unknown source in Osaka, Japan

A case of infant botulism of unknown origin, not involved in honey consumption, occurred in Osaka, Japan in 2020. A Clostridium botulinum type B strain named Osaka2020 was isolated from a stool sample of the patient. To clarify the epidemiology of the case, we performed whole-genome sequencing (WGS) of the isolate and compared it with strains from other sources. WGS analysis revealed that isolate Osaka2020 was classified into ST133 of a new sequence type, B5 subtype, and its toxin gene was encoded in a ∼274 kb plasmid. This plasmid was closely related to the pCLJ plasmid from strain 657Ba in the USA, reported to be conjugatively transferable to other strains. Moreover, isolate Osaka2020 also possesses another smaller plasmid that was common with some type A(B) infant botulism isolates in Japan. The phylogenetic tree from whole-genome SNP analysis showed that isolate Osaka2020 was the most closely related to a type B infant botulism isolate that occurred in Japan 10 years ago. Although no epidemiological connection among the two cases was confirmed, there is possibility that the cases are attributed to common causes such as some environmental substance.

Biofilm formation and genomic features of Listeria monocytogenes strains isolated from meat and dairy industries located in Piedmont (Italy)

Listeria monocytogenes is considered a major challenge for the food industry as it can persist for long periods in food processing plants by forming biofilms. The aims of this study were: i) to assess the biofilm producing ability of 57 Listeria monocytogenes isolates previously subjected to whole-genome sequencing (WGS); ii) to compare the levels of biofilm formation with the presence or absence of biofilm associated genes. To determine the presence or absence of a known set of biofilm associated genes, a comparative genomic analysis was performed on each strain. Among Listeria monocytogenes isolates, 58 %, 38.5 % and 3.5 % exhibited weak, moderate or strong biofilm production, respectively. No difference in biofilm production was observed between food and environmental isolates. The percentage of Listeria monocytogenes strains isolated from meat products (57 %) classified as moderate or strong biofilm producers was higher than the percentage obtained for strains isolated from dairy products (28 %). The presence of the Stress Survival Islet 1, the arsD stress gene and the truncated inlA protein was significantly associated with increased levels of biofilm. Combining biofilm phenotype with molecular and genotyping data may provide the opportunity to better understand the relationship between genes linked to biofilm formation in Listeria monocytogenes.

In-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region

Endophytic strains belonging to the Bacillus cereus group were isolated from the halophytes Atriplex halimus L. (Amaranthaceae) and Tamarix aphylla L. (Tamaricaceae) from costal and continental regions in Algeria. Based on their salt tolerance (up to 5%), the strains were tested for their ability to alleviate salt stress in tomato and wheat. Bacillus sp. strain BH32 showed the highest potential to reduce salinity stress (up to + 50% and + 58% of dry weight improvement, in tomato and wheat, respectively, compared to the control). To determine putative mechanisms involved in salt tolerance and plant growth promotion, the whole genome of Bacillus sp. BH32 was sequenced, annotated, and used for comparative genomics against the genomes of closely related strains. The pangenome of Bacillus sp. BH32 and its closest relative was further analyzed. The phylogenomic analyses confirmed its taxonomic position, a member of the Bacillus cereus group, with intergenomic distances (GBDP analysis) pinpointing to a new taxon (digital DNA-DNA hybridization, dDDH < 70%). Genome mining unveiled several genes involved in stress tolerance, production of anti-oxidants and genes involved in plant growth promotion as well as in the production of secondary metabolites. KEY POINTS : • Bacillus sp. BH32 and other bacterial endophytes were isolated from halophytes, to be tested on tomato and wheat and to limit salt stress adverse effects. • The strain with the highest potential was then studied at the genomic level to highlight numerous genes linked to plant growth promotion and stress tolerance. • Pangenome approaches suggest that the strain belongs to a new taxon within the Bacillus cereus group.

Distribution and identification of Mycobacterium tuberculosis lineage in Kashgar prefecture

Objectives

Kashgar prefecture is an important transportation and trade hub with a high incidence of tuberculosis. The following study analyzed the composition and differences in Mycobacterium tuberculosis (M.tb) lineage and specific tags to distinguish the lineage of the M.tb in Kashgar prefecture, thus providing a basis for the classification and diagnosis of tuberculosis in this area.

Methods

Whole-genome sequencing (WGS) of 161 M.tb clinical strains was performed. The phylogenetic tree was constructed using Maximum Likelihood (ML) based on single nucleotide polymorphisms (SNPs) and verified through principal component analysis (PCA). The composition structure of M.tb in different regions was analyzed by combining geographic information.

Results

M.tb clinical strains were composed of lineage 2 (73/161, 45.34%), lineage 3 (52/161, 32.30%) and lineage 4 (36/161, 22.36%). Moreover, the 3 lineages were subdivided into 11 sublineages, among which lineage 2 included lineage 2.2.2/Asia Ancestral 1 (9/73, 12.33%), lineage 2.2.1-Asia Ancestral 2 (9/73, 12.33%), lineage 2.2.1-Asia Ancestral 3 (18/73, 24.66%), and lineage 2.2.1-Modern Beijing (39/73, 53.42%). Lineage 3 included lineage 3.2 (14/52, 26.92%) and lineage 3.3 (38/52, 73.08%), while lineage 4 included lineage 4.1 (3/36, 8.33%), lineage 4.2 (2/36, 5.66%), lineage 4.4.2 (1/36, 2.78%), lineage 4.5 (28/36, 77.78%) and lineage 4.8 (2/36, 5.66%), all of which were consistent with the PCA results. One hundred thirty-six markers were proposed for discriminating known circulating strains. Reconstruction of a phylogenetic tree using the 136 SNPs resulted in a tree with the same number of delineated clades. Based on geographical location analysis, the composition of Lineage 2 in Kashgar prefecture (45.34%) was lower compared to other regions in China (54.35%-90.27%), while the composition of Lineage 3 (32.30%) was much higher than in other regions of China (0.92%-2.01%), but lower compared to the bordering Pakistan (70.40%).

Conclusion

Three lineages were identified in M.tb clinical strains from Kashgar prefecture, with 136 branch-specific SNP. Kashgar borders with countries that have a high incidence of tuberculosis, such as Pakistan and India, which results in a large difference between the M.tb lineage and sublineage distribution in this region and other provinces of China.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07307-4.

A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses

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Robust method for the genomic characterization of all Capripoxviruses.

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Pre-sequencing enrichment method based on targeted long-range PCR amplification.

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Method applicable to low titre samples such as blood samples and vaccine batches.

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Viral DNA enrichment compatible with various sample types and sequencing platforms.

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Complete coding genome sequencing evaluated on three different sequencing platforms.

The diseases caused by capripoxviruses (CaPVs) are of major economic concern in sheep, goat and cattle as they are inexorably spreading into non-endemic regions. As CaPV strains are serologically indistinguishable and genetically highly homologous, typing closely related strains can only be achieved by whole genome sequencing. Unfortunately the number of publicly available genomes remains low as most sequencing methods rely on virus isolation. Therefore, we developed a robust, cost-effective and widely applicable method that allows to generate (nearly) complete CaPV genomes directly from clinical samples or commercial vaccine batches. A set of pan-CaPVs long-range PCRs spanning the entire genome was designed to generate PCR amplicons that can be sequenced on commonly used high-throughput sequencing platforms: MiSeq (Illumina), RSII (PacBio) and MinION (Oxford Nanopore Technologies). The robustness of the LR-PCR strategy was evaluated for all 3 members of CaPV directly from a variety of samples, including clinical samples (N = 7), vaccine batches (N = 6), and virus isolates (N = 2). The sequencing method described here allows to reconstruct (nearly) complete CaPV genomes in less than a week and will aid researchers studying closely-related CaPV strains worldwide.

MycoSNP: A Portable Workflow for Performing Whole-Genome Sequencing Analysis of Candida auris

Candida auris is an urgent public health threat characterized by high drug-resistant rates and rapid spread in healthcare settings worldwide. As part of the C. auris response, molecular surveillance has helped public health officials track the global spread and investigate local outbreaks. Here, we describe whole-genome sequencing analysis methods used for routine C. auris molecular surveillance in the United States; methods include reference selection, reference preparation, quality assessment and control of sequencing reads, read alignment, and single-nucleotide polymorphism calling and filtration. We also describe the newly developed pipeline MycoSNP, a portable workflow for performing whole-genome sequencing analysis of fungal organisms including C. auris.

Functional Studies of Genetic Variants Associated with Human Diseases in Notch Signaling-Related Genes Using Drosophila

Rare variants in the many genes related to Notch signaling cause diverse Mendelian diseases that affect myriad organ systems. In addition, genome- and exome-wide association studies have linked common and rare variants in Notch-related genes to common diseases and phenotypic traits. Moreover, somatic mutations in these genes have been observed in many types of cancer, some of which are classified as oncogenic and others as tumor suppressive. While functional characterization of some of these variants has been performed through experimental studies, the number of "variants of unknown significance" identified in patients with diverse conditions keeps increasing as high-throughput sequencing technologies become more commonly used in the clinic. Furthermore, as disease gene discovery efforts identify rare variants in human genes that have yet to be linked to a disease, the demand for functional characterization of variants in these "genes of unknown significance" continues to increase. In this chapter, we describe a workflow to functionally characterize a rare variant in a Notch signaling related gene that was found to be associated with late-onset Alzheimer's disease. This pipeline involves informatic analysis of the variant of interest using diverse human and model organism databases, followed by in vivo experiments in the fruit fly Drosophila melanogaster. The protocol described here can be used to study variants that affect amino acids that are not conserved between human and fly. By "humanizing" the almondex gene in Drosophila with mutant alleles and heterologous genomic rescue constructs, a missense variant in TM2D3 (TM2 Domain Containing 3) was shown to be functionally damaging. This, and similar approaches, greatly facilitate functional interpretations of genetic variants in the human genome and propel personalized medicine.

High production of egc2-related staphylococcal enterotoxins caused a food poisoning outbreak

Staphylococcal enterotoxins (SEs) produced by enterotoxigenic Staphylococcus aureus in food cause staphylococcal food poisoning. We recently reported a foodborne outbreak due to S. aureus harboring new SE/SE-like (SEl) genes (seg, sei, sem, sen, seo, and selu) related to enterotoxin gene cluster (egc) 2 as with other research groups. However, the pathogenicity of SEs production remains unclear. Therefore, we herein investigated egc2-related SEs production from S. aureus isolates and leftover food items during a foodborne outbreak using a sandwich enzyme-linked immunosorbent assay suitable for the quantification of SEs. S. aureus isolates produced markedly high levels of egc2-related SEs, and the leftover food item "Sushi" contained SEs over the toxin dose that causes food poisoning symptoms. A representative isolate was subjected to whole-genome sequencing. The isolate was homologous with previously reported ST45 strains, particularly the unique genomic island νSaβ structure mostly consisting of egc2. The present study indicates that egc2-related SEs are food poisoning causative agents based on high SE production levels within an actual foodborne outbreak.

Seven novel glucose-6-phosphate dehydrogenase (G6PD) deficiency variants identified in the Qatari population

Background

Glucose-6-phosphate dehydrogenase deficiency (G6PDD) is the most common red cell enzymopathy in the world. In Qatar, the incidence of G6PDD is estimated at around 5%; however, no study has investigated the genetic basis of G6PDD in the Qatari population yet.

Methods

In this study, we analyzed whole-genome sequencing data generated by the Qatar Genome Programme for 6045 Qatar Biobank participants, to identify G6PDD variants in the Qatari population. In addition, we assessed the impact of the novel variants identified on protein function both in silico and by measuring G6PD enzymatic activity in the subjects carrying them.

Results

We identified 375 variants in/near G6PD gene, of which 20 were high-impact and 16 were moderate-impact variants. Of these, 14 were known G6PDD-causing variants. The most frequent G6PD-causing variants found in the Qatari population were p.Ser188Phe (G6PD Mediterranean), p.Asn126Asp (G6PD A +), p.Val68Met (G6PD Asahi), p.Ala335Thr (G6PD Chatham), and p.Ile48Thr (G6PD Aures) with allele frequencies of 0.0563, 0.0194, 0.00785, 0.0050, and 0.00380, respectively. Furthermore, we have identified seven novel G6PD variants, all of which were confirmed as G6PD-causing variants and classified as class III variants based on the World Health Organization’s classification scheme.

Conclusions

This is the first study investigating the molecular basis of G6PDD in Qatar, and it provides novel insights about G6PDD pathogenesis and highlights the importance of studying such understudied population.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40246-021-00358-9.

Genomic insights into the emergence and spread of methicillin-resistant Staphylococcus pseudintermedius in veterinary clinics

Staphylococcus pseudintermedius is a common cause of skin and soft tissue infections in dogs but can also cause infections in cats and humans. The frequency of methicillin-resistant S. pseudintermedius (MRSP) strains is increasing worldwide. Here, we obtained 43 MRSP isolates from dogs (n = 41), one cat (n = 1) and the small animal clinic environment (n = 1) in Slovenia from the period 2008-2018, which underwent whole-genome sequencing (WGS) and antimicrobial susceptibility testing. Five sequence types (STs) were identified, with ST71 (32/43) and ST551 (8/43) being the predominant. In Slovenia, ST551 was first detected in 2016, whereas a decrease in the frequency of ST71 was observed after 2015. All isolates were multidrug-resistant and most antimicrobial-resistant phenotypes could be linked to acquisition of the corresponding resistance genes or gene mutations. Core-genome multilocus sequence typing (cgMLST) revealed several potential MRSP transmission routes: (i) between two veterinary clinics by a single MRSP-positive dog, (ii) between the environment of a veterinary clinic and a dog, and (iii) between a canine and a feline patient through the contaminated environment of a veterinary clinic. Of the six dogs that were additionally sampled from 14 days to five months after the initial sampling, each harbored the same MRSP strain, suggesting a limited within-host diversity of MRSP in symptomatic dogs. The present results highlight the importance of MRSP-positive dogs in the spread of veterinary care-associated MRSP infections and call for the implementation of strict control measures to reduce MRSP contamination in veterinary clinic environments originating from animal-contact surfaces.

Yersinia pestis strains isolated in natural plague foci of Caucasus and Transcaucasia in the context of the global evolution of species

BACKGROUND

Plague is a highly dangerous vector-borne infectious disease that has left a significant mark on history of humankind. There are 13 natural plague foci in the Caucasus, located on the territory of the Russian Federation, Azerbaijan, Armenia and Georgia. We performed whole-genome sequencing of Y. pestis strains, isolated in the natural foci of the Caucasus and Transcaucasia. Using the data of whole-genome SNP analysis and Bayesian phylogeny methods, we carried out an evolutionary-phylogeographic analysis of modern population of the plague pathogen in order to determine the phylogenetic relationships of Y. pestis strains from the Caucasus with the strains from other countries.

RESULTS

We used 345 Y. pestis genomes to construct a global evolutionary phylogenetic reconstruction of species based on whole-genome SNP analysis. The genomes of 16 isolates were sequenced in this study, the remaining 329 genomes were obtained from the GenBank database. Analysis of the core genome revealed 3315 SNPs that allow differentiation of strains. The evolutionary phylogeographic analysis showed that the studied Y. pestis strains belong to the genetic lineages 0.PE2, 2.MED0, and 2.MED1. It was shown that the Y. pestis strains isolated on the territory of the East Caucasian high-mountain, the Transcaucasian high-mountain and the Priaraksinsky low-mountain plague foci belong to the most ancient of all existing genetic lineages - 0.PE2.

CONCLUSIONS

On the basis of the whole-genome SNP analysis of 345 Y. pestis strains, we describe the modern population structure of the plague pathogen and specify the place of the strains isolated in the natural foci of the Caucasus and Transcaucasia in the structure of the global population of Y. pestis. As a result of the retrospective evolutionary-phylogeographic analysis of the current population of the pathogen, we determined the probable time frame of the divergence of the genetic lineages of Y. pestis, as well as suggested the possible paths of the historical spread of the plague pathogen.

Whole-genome sequencing of Egyptian multidrug-resistant Klebsiella pneumoniae isolates: a multi-center pilot study

Multidrug-resistant (MDR) Klebsiella pneumoniae is a common infectious pathogen. We performed whole-genome sequencing (WGS) of 39 randomly selected, geographically diverse MDR K. pneumoniae from nine Egyptian hospitals. Clinical sources, phenotypic antibiotic resistance, and hyper-mucoviscosity were documented. WGS data were epidemiologically interpreted and tested for the presence of antibiotic resistance and virulence genes. Based on WGS data, we identified 18 classical multi-locus sequence types (MLST), the most common type being ST101 (23.1%) followed by ST147 (17.9%). Phylogenetic analyses identified small numbers of closely related isolates in a few of the centers, so we mostly documented independent nosocomial acquisition or import from public sources. The most common acquired resistance gene found was bla_CTX-M-15, detected in 27 isolates (69.2%). Carbapenemase genes encountered were bla_NDM-1 (n = 13), bla_NDM-5 (n = 1), bla_OXA-48 (n = 12), bla_OXA-181 (n = 2), and bla_KPC2 (n = 1). Seven strains (18%) contained more than a single carbapenemase gene. While searching for virulence-associated genes, sixteen wzi alleles were identified with wzi137, wzi64, and wzi50 most commonly found in ST101, ST147, and ST16, respectively. Yersiniabactin was the most common virulence factor (69.2%). Hyper-mucoviscosity was documented for 6 out of 39 isolates.This is the first genomic study of MDR K. pneumoniae from Egypt. The study revealed a clear spread of well-known international clones and their associated antimicrobial resistance and (hyper)virulence traits. The clinical situation in Egypt seems to reflect the scenario documented in many other countries and requires close attention.

Unexpected Mycoplasma hominis infection in two renal transplant recipients traced back to the same donor by whole-genome sequencing

Mycoplasma hominis is a common colonizer of the lower genitourinary tract. Although its clinical relevance for causing urogenital infections in immunocompetent individuals is controversial, this bacterium has been involved in severe invasive infections in allograft recipients. In this report, we describe two cases of M. hominis infection in two young renal transplant recipients within the first month post-transplant. Although at first no epidemiological link between the two cases had been suspected, whole-genome sequencing (WGS) analysis showed that both isolates were identical, highly suggestive of an origin with the common organ donor.

Performance of copy number variants detection based on whole-genome sequencing by DNBSEQ platforms

BACKGROUND

DNBSEQ™ platforms are new massively parallel sequencing (MPS) platforms that use DNA nanoball technology. Use of data generated from DNBSEQ™ platforms to detect single nucleotide variants (SNVs) and small insertions and deletions (indels) has proven to be quite effective, while the feasibility of copy number variants (CNVs) detection is unclear.

RESULTS

Here, we first benchmarked different CNV detection tools based on Illumina whole-genome sequencing (WGS) data of NA12878 and then assessed these tools in CNV detection based on DNBSEQ™ sequencing data from the same sample. When the same tool was used, the CNVs detected based on DNBSEQ™ and Illumina data were similar in quantity, length and distribution, while great differences existed within results from different tools and even based on data from a single platform. We further estimated the CNV detection power based on available CNV benchmarks of NA12878 and found similar precision and sensitivity between the DNBSEQ™ and Illumina platforms. We also found higher precision of CNVs shorter than 1 kbp based on DNBSEQ™ platforms than those based on Illumina platforms by using Pindel, DELLY and LUMPY. We carefully compared these two available benchmarks and found a large proportion of specific CNVs between them. Thus, we constructed a more complete CNV benchmark of NA12878 containing 3512 CNV regions.

CONCLUSIONS

We assessed and benchmarked CNV detections based on WGS with DNBSEQ™ platforms and provide guidelines for future studies.

Next-Generation Sequencing in Clinical Microbiology: Are We There Yet?

Next-generation sequencing (NGS) applications have been transitioning from research tools to diagnostic methods and are becoming more commonplace in clinical microbiology laboratories. These applications include (1) whole-genome sequencing, (2) targeted next-generation sequencing methods, and (3) metagenomic next-generation sequencing. The introduction of these methods into the clinical microbiology laboratory has led to the theoretic question of "Will NGS-based methods supplant traditional methods for strain typing, identification, and antimicrobial susceptibility prediction?" The authors address this question and discuss where we are at now with clinical NGS applications for infectious diseases, what does the future hold, and at what cost?

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture

Background

The microbiome of the oral cavity is the second-largest and diverse microbiota after the gut, harboring over 700 species of bacteria and including also fungi, viruses, and protozoa. With its diverse niches, the oral cavity is a very complex environment, where different microbes preferentially colonize different habitats. Recent data indicate that the oral microbiome has essential functions in maintaining oral and systemic health, and the emergence of 16S rRNA gene next-generation sequencing (NGS) has greatly contributed to revealing the complexity of its bacterial component. However, a detailed site-specific map of oral microorganisms (including also eukaryotes and viruses) and their relative abundance is still missing. Here, we aimed to obtain a comprehensive view of the healthy oral microbiome (HOM), including its drug-resistance features.

Results

The oral microbiome of twenty healthy subjects was analyzed by whole-genome sequencing (WGS) and real-time quantitative PCR microarray. Sampled oral micro-habitat included tongue dorsum, hard palate, buccal mucosa, keratinized gingiva, supragingival and subgingival plaque, and saliva with or without rinsing. Each sampled oral niche evidenced a different microbial community, including bacteria, fungi, and viruses. Alpha-diversity evidenced significant differences among the different sampled sites (p < 0.0001) but not among the enrolled subjects (p = 0.876), strengthening the notion of a recognizable HOM. Of note, oral rinse microbiome was more representative of the whole site-specific microbiomes, compared with that of saliva. Interestingly, HOM resistome included highly prevalent genes conferring resistance to macrolide, lincosamides, streptogramin, and tetracycline.

Conclusions

The data obtained in 20 subjects by WGS and microarray analysis provide for the first time a comprehensive view of HOM and its resistome, contributing to a deeper understanding of the composition of oral microbiome in the healthy subject, and providing an important reference for future studies, allowing to identify microbial signatures related to functional and metabolic alterations associated with diseases, potentially useful for targeted therapies and precision medicine.

Retrospective investigation of listeriosis outbreaks in small ruminants using different analytical approaches for whole genome sequencing-based typing of Listeria monocytogenes

Listeria monocytogenes is the causative agent of listeriosis, a serious disease affecting both humans and animals. While listeriosis outbreaks in humans are commonly investigated in detail, routine typing of L. monocytogenes is generally not performed in animal outbreaks. Here, seven presumable listeriosis outbreaks in small ruminants were retrospectively identified based on the pulsed-field gel electrophoresis (PFGE) profiles. Outbreaks were further characterised using three different analytical approaches based on the whole-genome sequencing (WGS) data: core-genome multilocus sequence typing (cgMLST), whole-genome MLST (wgMLST) and whole-genome single nucleotide polymorphism (wgSNP) typing. A monoclonal pattern of all seven outbreaks was identified using all three approaches, indicating common-source outbreaks. The outbreak strains belonged to sequence types (STs) 1 (n = 3), ST18 (n = 1), ST21 (n = 2) and ST184 (n = 1). Two epidemiologically linked ST1 outbreaks with indistinguishable PFGE profiles showed a polyphyletic nature and differed in >78 SNPs; thus, they were classified as separate outbreaks according to WGS. In ST184, the outbreak strain was also found in faeces of apparently healthy ruminants, silage and water collected from the trough, which were the most likely source(s) of infection. The outbreak-associated isolates differed in 0-7 cgMLST alleles, 0-12 wgMLST alleles and 1-13 SNPs. The minimum genetic diversity between outbreak-associated isolates and epidemiologically unrelated isolates of the same ST was low in all analysed cases, approaching the maximum diversity within the outbreak cluster. The results suggest that a fixed threshold to define the outbreak cluster should only be considered as a guide and highlight the role of epidemiological data for outbreak confirmation. The identified cgMLST clusters may be further investigated by wgMLST and/or wgSNP typing to increase confidence during investigations of outbreaks caused by highly clonal L. monocytogenes groups. This study gives an overview of the inter- and intra-outbreak genetic diversity of L. monocytogenes strains involved in animal outbreaks, hence improving their investigation.

Molecular Typing of Candida glabrata

The yeast Candida glabrata has emerged, second only to Candida albicans, to be one of the most frequently isolated fungi in clinical specimen from human. Its frequent resistance towards azole antifungal drugs and the high capacity to form biofilms on indwelling catheters of individual isolates render it an often difficult to treat pathogen. Hence, there is a notably increasing scientific and clinical interest in this species. This has led to the development of a variety of molecular tools for genetic modification, strain collections, and last but not least different approaches to analyse the population structure among isolates of different geographical and clinical contexts. Often, these are used to study correlations (or the absence thereof) with different pathogenicity, virulence, or drug resistance traits. Three molecular methods have been used to type within the C. glabrata population on a genetic level by multiple studies: multi-locus sequence typing, microsatellite length polymorphisms, and clustering of whole-genome sequencing data, and these are subject of this review.

Real-time whole genome sequencing to control a Streptococcus pyogenes outbreak at a national orthopaedic hospital

BACKGROUND

Whole genome sequencing (WGS) of Streptococcus pyogenes linked to invasive disease has been used to identify and investigate outbreaks. The clinical application of WGS in real-time for outbreak control is seldom employed.

AIMS

A fatal case of bacteraemia at a national orthopaedic hospital prompted an outbreak investigation to identify carriers and halt transmission using real-time WGS.

METHODS

Retrospective surveillance was conducted to identify patients with Streptococcus pyogenes infections in the last year. Upon contact tracing, four patients and 179 staff were screened for Streptococcus pyogenes carriage. All isolates identified were emm-typed. WGS was performed in real-time on a subset of isolates.

FINDINGS

Twelve isolates of Streptococcus pyogenes from the index case, two patients and eight staff were identified. Six isolates were emm 1.0, including the index case and five staff isolates. The remaining isolates belonged to distinct emm types. WGS analysis was undertaken on the six emm 1.0 isolates. Five were indistinguishable by single nucleotide polymorphism (SNP) analysis, with 0 SNP distance, and one had one SNP difference, supporting the hypothesis of recent local transmission. All screen-positive healthcare workers were offered treatment with penicillin or clindamycin. No further cases were identified.

CONCLUSION

The increased molecular discrimination of WGS confirmed the clustering of these cases and the outbreak was contained. This demonstrates the clinical utility of WGS in managing outbreaks of invasive Streptococcus pyogenes in real-time and we recommend its implementation as a routine clinical service.

Gen2Epi: an automated whole-genome sequencing pipeline for linking full genomes to antimicrobial susceptibility and molecular epidemiological data in Neisseria gonorrhoeae

BACKGROUND

Recent adva1nces in whole genome sequencing (WGS) based technologies have facilitated multi-step applications for predicting antimicrobial resistance (AMR) and investigating the molecular epidemiology of Neisseria gonorrhoeae. However, generating full scaffolds of N. gonorrhoeae genomes from short reads, and the assignment of molecular epidemiological information (NG-MLST, NG-MAST, and NG-STAR) to multiple assembled samples, is challenging due to required manual tasks such as annotating antimicrobial resistance determinants with standard nomenclature for a large number of genomes.

RESULTS

We present Gen2Epi, a pipeline that assembles short reads into full scaffolds and automatically assigns molecular epidemiological and AMR information to the assembled genomes. Gen2Epi is a command-line tool integrating third-party software and tailored specifically for N. gonorrhoeae. For its evaluation, the Gen2Epi pipeline successfully assembled the WGS short reads from 1484 N. gonorrhoeae samples into full-length genomes for both chromosomes and plasmids and was able to assign in silico molecular determinant information to each dataset automatically. The assemblies were generated using raw as well as trimmed short reads. The median genome coverage of full-length scaffolds and "N" statistics (N50, NG50, and NGA50) were higher than, or comparable to, previously published results and the scaffolding process improved the quality of the draft genome assemblies. Molecular antimicrobial resistant (AMR) determinants identified by Gen2Epi reproduced information for the 1484 samples as previously reported, including NG-MLST, NG-MAST, and NG-STAR molecular sequence types.

CONCLUSIONS

Gen2Epi can be used to assemble short reads into full-length genomes and assign accurate molecular marker and AMR information automatically from NG-STAR, NG-MAST, and NG-MLST. Gen2Epi is publicly available under "CC BY-NC 2.0 CA" Creative Commons licensing as a VirtualBox image containing the constituent software components running on the LINUX operating system (CentOS 7). The image and associated documentation are available via anonymous FTP at ftp://www.cs.usask.ca/pub/combi or ftp://ftp.cs.usask.ca/pub/combi.

Application of Whole-Genome Sequencing to Transposon Mutants of Salmonella Heidelberg

Transposons are elements widely dispersed among organisms which are able to move and replicate fragments of genomes. The extensive variability in transposons present in most organisms requires extensive identification and interpretation of the resulting transposon mutants after transposon mutagenesis. However, much of this is reliant on utilizing randomness characteristics of transposon to identify essential genes for the organism of interest. Integration of the transposon mutant approach with commercialized next-generation sequencing (NGS) technology has helped to advance transposon identification by sequencing millions of reads generated from a single run on an NGS platform. Transposon sequencing is defined as a gene sequencing methodology that allows for the identification of nonessential genes and the determination of gene function using a random transposon insertional mutagenesis followed by massively parallel sequencing. The detailed protocol will be outlined in this chapter. The genomic DNA integrated with the transposons is sequenced using an NGS platform in order to determine the location of each mutation.

Clonal or not clonal? Investigating hospital outbreaks of KPC-producing Klebsiella pneumoniae with whole-genome sequencing

OBJECTIVES

Whole-genome sequencing (WGS) is a promising tool for identifying transmission pathways in outbreaks caused by multidrug-resistant bacteria. However, it is uncertain how the data produced by WGS can be best integrated into epidemiologic investigations.

METHODS

We tested various genomic analyses to identify clonal groups in two distinct outbreaks of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae that occurred in Switzerland in 2013 and 2015. In blinded fashion, we sequenced 12 strains involved in the two outbreaks, respectively, and six that were epidemiologically unrelated. We analysed genomic commonalities from conserved genes to plasmid-borne antibiotic resistance genes (ARGs) and contrasted these results with available epidemiologic evidence.

RESULTS

Using WGS, blinded analysts correctly identified the two clusters of strains from the two outbreaks. Nonetheless, the 2015 index strain was found to be slightly different (1-3 single nucleotide variants) from the strains recovered from secondary cases, likely because prior long-term carriage (3 years) by the index patient allowed for genetic mutations over time. Also, we observed occasional loss of ARG-bearing plasmidic fragments in outbreak-causing strains.

CONCLUSIONS

Retrospective WGS analysis was successful in identifying clonal groups in both outbreaks. Still, data should be analysed with caution in cases of previous long-term carriage of the studied bacteria.

Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary

Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary .