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Asset Tag: Human pathogen

July 7, 2019

Molecular evolution of a Klebsiella pneumoniae ST278 isolate harboring blaNDM-7 and involved in nosocomial transmission.

During 2013, ST278 Klebsiella pneumoniae with blaNDM-7 was isolated from the urine (KpN01) and rectum (KpN02) of a patient in Calgary, Canada. The same strain (KpN04) was subsequently isolated from another patient in the same unit. Interestingly, a carbapenem-susceptible K. pneumoniae ST278 (KpN06) was obtained 1 month later from the blood of the second patient. Next-generation sequencing (NGS) revealed that the loss of carbapenem-resistance in KpN06 was due to a 5-kb deletion on the blaNDM-7-harboring IncX3 plasmid. In addition, an IncFIB plasmid in KpN06 had a 27-kb deletion that removed genes encoding for heavy metal resistance. Phylogenetic analysis showed that the K. pneumoniae ST278 from patient 2 was likely a descendant of KpN02 and that KpN06 was a close progenitor of an environmental ST278. It is unclear whether KpN06 lost the blaNDM-7 gene in vivo. This study detailed the remarkable plasticity and speed of evolutionary changes in multidrug-resistant K. pneumoniae, demonstrating the highly recombinant nature of this species. It also highlights the ability of NGS to clarify molecular microevolutionary events within antibiotic-resistant organisms.© The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

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July 7, 2019

Salmonella degrades the host glycocalyx leading to altered infection and glycan remodeling.

Complex glycans cover the gut epithelial surface to protect the cell from the environment. Invasive pathogens must breach the glycan layer before initiating infection. While glycan degradation is crucial for infection, this process is inadequately understood. Salmonella contains 47 glycosyl hydrolases (GHs) that may degrade the glycan. We hypothesized that keystone genes from the entire GH complement of Salmonella are required to degrade glycans to change infection. This study determined that GHs recognize the terminal monosaccharides (N-acetylneuraminic acid (Neu5Ac), galactose, mannose, and fucose) and significantly (p?

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July 7, 2019

Plasmid-mediated colistin resistance in a patient infected with Klebsiella pneumoniae.

It is alarming that the plasmid-mediated mcr-1-encoded colistin resistance discovered by Yi-Yun Liu and colleagues,1 probably selected in cows and pigs as discussed by Marisa Haenni and colleagues2 and Surbhi Malhorta-Kumar and colleagues,3 is now spreading globally in Gram-negative pathogens.4 Moreover, colistin-resistant Escherichia coli without the canonical mcr-1 gene suggest that other (transferable) colistin-resistant mechanisms exist.3

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July 7, 2019

Complete genome sequence of Plesiomonas shigelloides type strain NCTC10360.

Plesiomonas shigelloides is a Gram-negative rod within the Enterobacteriaceae family. It is a gastrointestinal pathogen of increasing notoriety, often associated with diarrheal disease. P. shigelloides is waterborne, and infection is often linked to the consumption of seafood. Here, we describe the first complete genome for P. shigelloides type strain NCTC10360.© Crown copyright 2016.

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July 7, 2019

Draft genome sequence of Escherichia coli S51, a chicken isolate harboring a chromosomally encoded mcr-1 gene.

We present the draft genome of Escherichia coli S51, a colistin-resistant extended-spectrum ß-lactamase-producing strain isolated in 2015 from raw chicken meat imported from Germany. Assembly and annotation of this draft genome resulted in a 4,994,918-bp chromosome and revealed a chromosomally encoded mcr-1 gene responsible for the colistin resistance of the strain. Copyright © 2016 Zurfluh et al.

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July 7, 2019

Lysosomal Cathepsin A plays a significant role in the processing of endogenous bioactive peptides.

Lysosomal serine carboxypeptidase Cathepsin A (CTSA) is a multifunctional enzyme with distinct protective and catalytic function. CTSA present in the lysosomal multienzyme complex to facilitate the correct lysosomal routing, stability and activation of with beta-galactosidase and alpha-neuraminidase. Beside CTSA has role in inactivation of bioactive peptides including bradykinin, substances P, oxytocin, angiotensin I and endothelin-I by cleavage of 1 or 2 amino acid(s) from C-terminal ends. In this study, we aimed to elucidate the regulatory role of CTSA on bioactive peptides in knock-in mice model of CTSA(S190A) . We investigated the level of bradykinin, substances P, oxytocin, angiotensin I and endothelin-I in the kidney, liver, lung, brain and serum from CTSA(S190A) mouse model at 3- and 6-months of age. Our results suggest CTSA selectively contributes to processing of bioactive peptides in different tissues from CTSA(S190A) mice compared to age matched WT mice.

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July 7, 2019

Full-genome sequence of Escherichia coli K-15KW01, a uropathogenic E. coli B2 sequence type 127 isolate harboring a chromosomally carried blaCTX-M-15 gene.

We present here the full-genome sequence of Escherichia coli K-15KW01, an extended-spectrum-ß-lactamase-producing uropathogenic strain. Assembly and annotation of the draft genome resulted in a 5,154,641-bp chromosome and revealed a chromosomally contained blaCTX-M-15 gene embedded at the right-hand extremity of an ISEcp1 element in a plasmid-like structure (36,907 bp). Copyright © 2016 Zurfluh et al.

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July 7, 2019

Complete genome sequence of Bordetella pertussis strain VA-190 isolated from a vaccinated 10-year-old patient with whooping cough.

The number of cases of pertussis has increased in the United States despite vaccination. We present the genome of an isolate of Bordetella pertussis from a vaccinated patient from Virginia. The genome was sequenced by long-read methodology and compared to that of a clinical isolate used for laboratory studies, D420. Copyright © 2016 Eby et al.

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July 7, 2019

The effects of signal erosion and core genome reduction on the identification of diagnostic markers.

Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives.A comparative analysis of 1,130 Burkholderia genomes identified unique markers for many named species, including the human pathogens B. pseudomallei and B. mallei Due to core genome reduction and signature erosion, only 38 targets specific to B. pseudomallei/mallei were identified. By using only public genomes, a larger number of markers were identified, due to undersampling, and this larger number represents the potential for false positives. This analysis has implications for the design of diagnostics for other species where the genomic space of the target and/or closely related species is not well defined. Copyright © 2016 Sahl et al.

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July 7, 2019

Complete genome sequence of Neisseria weaveri strain NCTC13585.

Neisseria weaveri is a commensal organism of the canine oral cavity and an occasional opportunistic human pathogen which is associated with dog bite wounds. Here we report the first complete genomic sequence of the N. weaveri NCTC13585 (CCUG30381) strain, which was originally isolated from a patient with a canine bite wound. Copyright © 2016 Alexander et al.

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July 7, 2019

Complete genome sequences of 17 Canadian isolates of Salmonella enterica subsp. enterica serovar Heidelberg from human, animal, and food sources.

Salmonella enterica subsp. enterica serovar Heidelberg is a highly clonal serovar frequently associated with foodborne illness. To facilitate subtyping efforts, we report fully assembled genome sequences of 17 Canadian S Heidelberg isolates including six pairs of epidemiologically related strains. The plasmid sequences of eight isolates contain several drug resistance genes. © Crown copyright 2016.

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July 7, 2019

Genome sequences of Ralstonia insidiosa type strain ATCC 49129 and strain FC1138, a strong biofilm producer isolated from a fresh-cut produce-processing plant.

Ralstonia insidiosa is an opportunistic pathogen and a strong biofilm producer. Here, we present the complete genome sequences of R. insidiosa FC1138 and ATCC 49129. Both strains have two circular chromosomes of approximately 3.9 and 1.9 Mb and a 50-kb plasmid. ATCC 49129 also possesses a megaplasmid of approximately 318 kb. Copyright © 2016 Xu et al.

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July 7, 2019

Complete genome sequence of Serratia marcescens U36365, a green pigment–producing strain isolated from a patient with urinary tract infection.

Serratia marcescens is an emerging nosocomial pathogen associated with urinary and respiratory tract infections. In this study, we determined the genome of a green pigment-producing clinical strain, U36365, isolated from a hospital in Southern India. De novo assembly of PacBio long-read sequencing indicates that the U36365 genome consists of a chromosome of 5.12 Mbps and no plasmids. Copyright © 2016 Sahni et al.

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