First description of arginine catabolic mobile element (ACME) type VI harboring the kdp operon only in Staphylococcus epidermidis using short and long read whole genome sequencing: Further evidence of ACME diversity

ABSTRACT The type III arginine catabolic mobile element (ACME) was detected in three Staphylococcus epidermidis oral isolates recovered from separate patients (one healthy, one healthy with dental implants, and one with periodontal disease) based on ACME-arc-operon- and ACME-opp3-operon-directed PCR. These isolates were subjected to whole-genome sequencing to characterize the precise structural organization of ACME III for the first time, which also revealed that all three isolates were the same sequence type, ST329.

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Genomic Analysis of Antibiotic-Resistant Staphylococcus epidermidis Isolates From Clinical Sources in the Kwazulu-Natal Province, South Africa

Frontiers in Microbiology ◽

10.3389/fmicb.2021.656306 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jonathan Asante ◽

Bakoena A. Hetsa ◽

Daniel G. Amoako ◽

Akebe L. K. Abia ◽

Linda A. Bester ◽

...

Keyword(s):

Antibiotic Resistance ◽

Multidrug Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Immune Evasion ◽

Staphylococcus Epidermidis ◽

Mobile Element ◽

Whole Genome ◽

Bioinformatics Analyses ◽

Modification System

Staphylococcus epidermidis has become an important nosocomial pathogen. Multidrug resistance makes S. epidermidis infections difficult to treat. The study aims to describe the genomic characteristics of methicillin-resistant S. epidermidis (MRSE) isolated from clinical sources, to comprehend the genetic basis of antibiotic resistance, virulence, and potential pathogenicity. Sixteen MRSE underwent whole-genome sequencing, and bioinformatics analyses were carried out to ascertain their resistome, virulome, mobilome, clonality, and phylogenomic relationships. In all, 75% of isolates displayed multidrug resistance and were associated with the carriage of multiple resistance genes including mecA, blaZ, tet(K), erm(A), erm(B), erm(C), dfrG, aac(6′)-aph(2′′), and cat(pC221) conferring resistance to β-lactams, tetracyclines, macrolide–lincosamide–streptogramin B, aminoglycosides, and phenicols, which were located on both plasmids and chromosomes. Their virulence profiles were evidenced by the presence of genes involved in adherence/biofilm formation (icaA, icaB, icaC, atl, ebh, and ebp), immune evasion (adsA, capC, and manA), and antiphagocytosis (rmlC, cdsA, and A). The community-acquired SCCmec type IV was the most common SCCmec type. The CoNS belonged to seven multilocus sequence types (MLSTs) and carried a diversity of mobile genetic elements such as phages, insertion sequences, and plasmids. The bacterial anti-phage defense systems clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) immunity phage system and restriction-modification system (R-M system) and the arginine catabolic mobile element (ACME) involved in immune evasion and transport of virulence genes were also found. The insertion sequence, IS256, linked with virulence, was found in 56.3% of isolates. Generally, the isolates clustered according to STs, with some similarity but also considerable variability within isolates. Whole-genome sequencing and bioinformatics analysis provide insights into the likely pathogenicity and antibiotic resistance of S. epidermidis, necessitating surveillance of this emerging pathogen.

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Long-read whole-genome sequencing identified a partial MBD5 deletion in an exome-negative patient with neurodevelopmental disorder

Journal of Human Genetics ◽

10.1038/s10038-020-00893-8 ◽

2021 ◽

Author(s):

Sachiko Ohori ◽

Rie S. Tsuburaya ◽

Masako Kinoshita ◽

Etsuko Miyagi ◽

Takeshi Mizuguchi ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Neurodevelopmental Disorder ◽

Whole Genome ◽

Negative Patient ◽

Long Read

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Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases

Journal of Human Genetics ◽

10.1038/s10038-018-0551-7 ◽

2018 ◽

Vol 64 (3) ◽

pp. 191-197 ◽

Cited By ~ 12

Author(s):

Takeshi Mizuguchi ◽

Tomoko Toyota ◽

Hiroaki Adachi ◽

Noriko Miyake ◽

Naomichi Matsumoto ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Repeat Expansion ◽

Whole Genome ◽

Smrt Sequencing ◽

Long Read

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Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0006566 ◽

2018 ◽

Vol 12 (6) ◽

pp. e0006566 ◽

Cited By ~ 11

Author(s):

Elizabeth M. Batty ◽

Suwittra Chaemchuen ◽

Stuart Blacksell ◽

Allen L. Richards ◽

Daniel Paris ◽

...

Keyword(s):

Comparative Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Orientia Tsutsugamushi ◽

Human Pathogen ◽

Long Read

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Multidrug-Resistant Proteus mirabilis Strain with Cointegrate Plasmid

Microorganisms ◽

10.3390/microorganisms8111775 ◽

2020 ◽

Vol 8 (11) ◽

pp. 1775

Author(s):

Andrey Shelenkov ◽

Lyudmila Petrova ◽

Valeria Fomina ◽

Mikhail Zamyatin ◽

Yulia Mikhaylova ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Proteus Mirabilis ◽

Intestinal Microflora ◽

Virulence Genes ◽

Multidrug Resistant ◽

Whole Genome ◽

Long Read ◽

Tract Infections ◽

Eskape Pathogens

Proteus mirabilis is a component of the normal intestinal microflora of humans and animals, but can cause urinary tract infections and even sepsis in hospital settings. In recent years, the number of multidrug-resistant P. mirabilis isolates, including the ones producing extended-spectrum β-lactamases (ESBLs), is increasing worldwide. However, the number of investigations dedicated to this species, especially, whole-genome sequencing, is much lower in comparison to the members of the ESKAPE pathogens group. This study presents a detailed analysis of clinical multidrug-resistant ESBL-producing P. mirabilis isolate using short- and long-read whole-genome sequencing, which allowed us to reveal possible horizontal gene transfer between Klebsiella pneumoniae and P. mirabilis plasmids and to locate the CRISPR-Cas system in the genome together with its probable phage targets, as well as multiple virulence genes. We believe that the data presented will contribute to the understanding of antibiotic resistance acquisition and virulence mechanisms for this important pathogen.

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Spill-Over from Public Health? First Detection of an OXA-48-Producing Escherichia coli in a German Pig Farm

Microorganisms ◽

10.3390/microorganisms8060855 ◽

2020 ◽

Vol 8 (6) ◽

pp. 855 ◽

Cited By ~ 2

Author(s):

Alexandra Irrgang ◽

Natalie Pauly ◽

Bernd-Alois Tenhagen ◽

Mirjam Grobbel ◽

Annemarie Kaesbohrer ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Bacterial Species ◽

Multidrug Resistant ◽

Meat Production ◽

Whole Genome ◽

Phenotypic Resistance ◽

Long Read ◽

Pig Farm ◽

Human Infections

Resistance to carbapenems is a severe threat to human health. These last resort antimicrobials are indispensable for the treatment of severe human infections with multidrug-resistant Gram-negative bacteria. In accordance with their increasing medical impact, carbapenemase-producing Enterobacteriaceae (CPE) might be disseminated from colonized humans to non-human reservoirs (i.e., environment, animals, food). In Germany, the occurrence of CPE in livestock and food has been systematically monitored since 2016. In the 2019 monitoring, an OXA-48-producing E. coli (19-AB01443) was recovered from a fecal sample of a fattening pig. Phenotypic resistance was confirmed by broth microdilution and further characterized by PFGE, conjugation, and combined short-/long-read whole genome sequencing. This is the first detection of this resistance determinant in samples from German meat production. Molecular characterization and whole-genome sequencing revealed that the blaOXA-48 gene was located on a common pOXA-48 plasmid-prototype. This plasmid-type seems to be globally distributed among various bacterial species, but it was frequently associated with clinical Klebsiella spp. isolates. Currently, the route of introduction of this plasmid/isolate combination into the German pig production is unknown. We speculate that due to its strong correlation with human isolates a transmission from humans to livestock has occurred.

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Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov

Genome Announcements ◽

10.1128/genomea.01057-17 ◽

2017 ◽

Vol 5 (42) ◽

Cited By ~ 15

Author(s):

S. Wesley Long ◽

Sarah E. Linson ◽

Matthew Ojeda Saavedra ◽

Concepcion Cantu ◽

James J. Davis ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Clinical Isolate ◽

Genome Sequencing ◽

Novel Species ◽

Whole Genome ◽

The Novel ◽

Short Read ◽

Oxford Nanopore ◽

Long Read

ABSTRACT In a study of 1,777 Klebsiella strains, we discovered KPN1705, which was distinct from all recognized Klebsiella spp. We closed the genome of strain KPN1705 using a hybrid of Illumina short-read and Oxford Nanopore long-read technologies. For this novel species, we propose the name Klebsiella quasivariicola sp. nov.

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Exploring the Missing Heritability in Subjects With Hearing Loss, Enlarged Vestibular Aqueducts, and A Single or No Pathogenic SLC26A4 Variant

10.21203/rs.3.rs-577715/v1 ◽

2021 ◽

Author(s):

Jeroen Smits ◽

Suzanne E. de Bruijn ◽

Cornelis P. Lanting ◽

Jaap Oostrik ◽

Luke O’Gorman ◽

...

Keyword(s):

Hearing Loss ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Mapping ◽

Copy Number Variants ◽

Whole Genome ◽

Missing Heritability ◽

Vestibular Aqueduct ◽

Pathogenic Variants ◽

Long Read

Abstract Pathogenic variants in SLC26A4 have been associated with autosomal recessive hearing loss (arHL) and a unilateral or bilateral enlarged vestibular aqueduct (EVA). SLC26A4 is the second most frequently mutated gene in arHL. Despite the strong genotype-phenotype correlation, a significant part of SLC26A4 cases remains genetically unresolved. In this study, we investigated a cohort of 28 Dutch index cases diagnosed with HL in combination with an EVA but without (M0) or with a single (M1) pathogenic variant in SLC26A4. To explore the missing heritability, short- and long-read whole genome sequencing and optical genome mapping were performed. We found a previously described EVA-associated haplotype (Caucasian EVA (CEVA)) to be significantly enriched in our M1 patient cohort. The haplotype was also present in two M0 cases. Despite extensive genetic analyses, we were not able to prioritize any of the variants present within the haplotype as the likely pathogenic defect, and therefore additional analyses addressing the defect(s) at the RNA, protein, or epigenetic level are required. Whole genome sequencing also revealed splice-altering SLC26A4 variants in two M1 cases, which are now genetically explained, but no deep-intronic or copy number variants. With these findings, we have provided important insights that will pave the way for elucidating the missing heritability in M0 and M1 SLC26A4 cases.

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Long-read sequencing across the C9orf72 ‘GGGGCC’ repeat expansion: implications for clinical use and genetic discovery efforts in human disease

10.1101/176651 ◽

2018 ◽

Cited By ~ 1

Author(s):

Mark T. W. Ebbert ◽

Stefan Farrugia ◽

Jonathon Sens ◽

Karen Jansen-West ◽

Tania F. Gendron ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Repeat Expansion ◽

Whole Genome ◽

Short Read ◽

Short Read Sequencing ◽

Sequencing Technologies ◽

Long Read ◽

Repeat Expansions ◽

Targeted Approach

AbstractBackground: Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 ‘GGGGCC’ (G4C2) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing technologies. It is unclear whether long-read sequencing technologies can traverse these long, challenging repeat expansions. Here, we demonstrate that two long-read sequencing technologies, Pacific Biosciences’ (PacBio) and Oxford Nanopore Technologies’ (ONT), can sequence through disease-causing repeats cloned into plasmids, including the FTD/ALS-causing G4C2 repeat expansion. We also report the first long-read sequencing data characterizing the C9orf72 G4C2 repeat expansion at the nucleotide level in two symptomatic expansion carriers using PacBio whole-genome sequencing and a no-amplification (No-Amp) targeted approach based on CRISPR/Cas9.Results: Both the PacBio and ONT platforms successfully sequenced through the repeat expansions in plasmids. Throughput on the MinlON was a challenge for whole-genome sequencing; we were unable to attain reads covering the human C9orf72 repeat expansion using 15 flow cells. We obtained 8x coverage across the C9orf72 locus using the PacBio Sequel, accurately reporting the unexpanded allele at eight repeats, and reading through the entire expansion with 1324 repeats (7941 nucleotides). Using the No-Amp targeted approach, we attained >800x coverage and were able to identify the unexpanded allele, closely estimate expansion size, and assess nucleotide content in a single experiment. We estimate the individual’s repeat region was >99% G4C2 content, though we cannot rule out small interruptions.Conclusions: Our findings indicate that long-read sequencing is well suited to characterizing known repeat expansions, and for discovering new disease-causing, disease-modifying, or risk-modifying repeat expansions that have gone undetected with conventional short-read sequencing. The PacBio No-Amp targeted approach may have future potential in clinical and genetic counseling environments. Larger and deeper long-read sequencing studies in C9orf72 expansion carriers will be important to determine heterogeneity and whether the repeats are interrupted by non-G4C2 content, potentially mitigating or modifying disease course or age of onset, as interruptions are known to do in other repeat-expansion disorders. These results have broad implications across all diseases where the genetic etiology remains unclear.

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