Whole-Genome Sequence Analysis of Antimicrobial Resistance Genes in Streptococcus uberis and Streptococcus dysgalactiae Isolates from Canadian Dairy Herds

Increasing antimicrobial resistance and limited alternative treatments have led to fluoroquinolone-resistant Shigella strain inclusion on the WHO global priority pathogens list. In this study we characterized multiple Shigella isolates from Malawi with whole genome sequence analysis, identifying the acquirable fluoroquinolone resistance determinant qnrS1.

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Whole genome sequence analysis of Shigella from Malawi identifies fluoroquinolone resistance

10.1101/2020.11.20.391235 ◽

2020 ◽

Author(s):

George E. Stenhouse ◽

Khuzwayo C. Jere ◽

Chikondi Peno ◽

Rebecca J. Bengtsson ◽

End Chinyama ◽

...

Keyword(s):

Sequence Analysis ◽

Antimicrobial Resistance ◽

Genome Sequence ◽

Resistance Determinant ◽

Whole Genome Sequence ◽

Fluoroquinolone Resistance ◽

Whole Genome ◽

Alternative Treatments ◽

Genome Sequence Analysis ◽

Global Priority

AbstractIncreasing antimicrobial resistance and limited alternative treatments led to fluoroquinolone resistant Shigella strain inclusion on the WHO global priority pathogens list. In this study we characterised multiple Shigella isolates from Malawi with whole genome sequence analysis, identifying the acquirable fluoroquinolone resistance determinant qnrS1.

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Whole Genome Sequencing of Staphylococci Isolated From Bovine Milk Samples

Frontiers in Microbiology ◽

10.3389/fmicb.2021.715851 ◽

2021 ◽

Vol 12 ◽

Author(s):

Marte Ekeland Fergestad ◽

Fabrice Touzain ◽

Sarne De Vliegher ◽

Anneleen De Visscher ◽

Damien Thiry ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Resistance Gene ◽

Resistance Genes ◽

Virulence Genes ◽

Bovine Milk ◽

Whole Genome Sequence ◽

Whole Genome ◽

Bacterial Survival ◽

Intramammary Infections ◽

Antimicrobial Resistance Genes

Staphylococci are among the commonly isolated bacteria from intramammary infections in bovines, where Staphylococcus aureus is the most studied species. This species carries a variety of virulence genes, contributing to bacterial survival and spread. Less is known about non-aureus staphylococci (NAS) and their range of virulence genes and mechanisms, but they are the most frequently isolated bacteria from bovine milk. Staphylococci can also carry a range of antimicrobial resistance genes, complicating treatment of the infections they cause. We used Illumina sequencing to whole genome sequence 93 staphylococcal isolates selected from a collection of staphylococcal isolates; 45 S. aureus isolates and 48 NAS isolates from 16 different species, determining their content of antimicrobial resistance genes and virulence genes. Antimicrobial resistance genes were frequently observed in the NAS species as a group compared to S. aureus. However, the lincosamide resistance gene lnuA and penicillin resistance gene blaZ were frequently identified in NAS, as well as a small number of S. aureus. The erm genes conferring macrolide resistance were also identified in several NAS isolates and in a small number of S. aureus isolates. In most S. aureus isolates, no antimicrobial resistance genes were detected, but in five S. aureus isolates three to six resistance genes were identified and all five of these carried the mecA gene. Virulence genes were more frequently identified in S. aureus, which contained on average five times more virulence genes compared to NAS. Among the NAS species there were also differences in content of virulence genes, such as S. chromogenes with a higher average number of virulence genes. By determining the content of a large selection of virulence genes and antimicrobial resistance genes in S. aureus and 16 different NAS species our results contribute with knowledge regarding the genetic basis for virulence and antimicrobial resistance in bovine staphylococci, especially the less studied NAS. The results can create a broader basis for further research into the virulence mechanisms of this important group of bacteria in bovine intramammary infections.

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Florfenicol Resistance in Enterobacteriaceae and Whole-Genome Sequence Analysis of Florfenicol-Resistant Leclercia adecarboxylata Strain R25

International Journal of Genomics ◽

10.1155/2019/9828504 ◽

2019 ◽

Vol 2019 ◽

pp. 1-10

Author(s):

Yuanyuan Ying ◽

Fei Wu ◽

Chongyang Wu ◽

Yi Jiang ◽

Min Yin ◽

...

Keyword(s):

Sequence Analysis ◽

Resistance Gene ◽

Genome Sequence ◽

Resistance Genes ◽

Mobile Genetic Elements ◽

Whole Genome Sequence ◽

Dilution Method ◽

Whole Genome ◽

Genome Sequence Analysis ◽

Genetic Elements

Due to inappropriate use, florfenicol resistance is becoming increasingly serious among animal respiratory tract and gut bacteria. To detect the florfenicol resistance mechanism among Enterobacteriaceae bacteria, 292 isolates from animal feces were examined. The agar dilution method was conducted to determine the minimum inhibitory concentration (MIC) for florfenicol, and polymerase chain reaction (PCR) was performed to detect florfenicol resistance genes. To further explore the molecular mechanism of florfenicol resistance, the whole-genome Leclercia adecarboxylata R25 was sequenced. Of the strains tested, 61.6% (180/292) were resistant to florfenicol, 64.4% (188/292) were positive for floR, and 1.0% (3/292) for cfr. The whole-genome sequence analysis of L. adecarboxylata R25 revealed that the floR gene is carried by a transposon and located on a plasmid (pLA-64). Seven other resistance genes are also encoded on pLA-64, all of which were found to be related to mobile genetic elements. The sequences sharing the greatest similarities to pLA-64 are the plasmids p02085-tetA of Citrobacter freundii and p234 and p388, both from Enterobacter cloacae. The resistance gene-related mobile genetic elements also share homologous sequences from different species or genera of bacteria. These findings indicate that floR mainly contributes to the high rate of florfenicol resistance among Enterobacteriaceae. The resistance gene-related mobile genetic elements encoded by pLA-64 may be transferred among bacteria of different species or genera, resulting in resistance dissemination.

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30-OR: Whole Genome Sequence Analysis of Type 2 Diabetes Risk in 44,713 Humans of Diverse Ancestry in the TOPMed Study

Diabetes ◽

10.2337/db19-30-or ◽

2019 ◽

Vol 68 (Supplement 1) ◽

pp. 30-OR

Author(s):

HEATHER M. HIGHLAND ◽

JENNIFER WESSEL ◽

ALISA MANNING ◽

Keyword(s):

Type 2 Diabetes ◽

Sequence Analysis ◽

Genome Sequence ◽

Diabetes Risk ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Analysis

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Recurrent Mycobacterium chelonae Skin Infection Unmasked as Factitious Disorder Using Bacterial Whole Genome Sequence Analysis

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa506 ◽

2020 ◽

Vol 7 (11) ◽

Author(s):

Sarah Flohr ◽

Alban Ramette ◽

Philipp K A Agyeman ◽

Andrea Duppenthaler ◽

Cordula Scherer ◽

...

Keyword(s):

Sequence Analysis ◽

Genome Sequence ◽

Surgical Therapy ◽

Skin Infection ◽

Whole Genome Sequence ◽

Factitious Disorder ◽

Whole Genome ◽

Mycobacterium Chelonae ◽

Genome Sequence Analysis ◽

Adequate Therapy

Abstract Mycobacterium chelonae infections usually resolve with adequate therapy. We report the case of an adolescent with a chronic and progressive M chelonae infection refractory to combined antimicrobial and surgical therapy. Whole genome sequence analysis of consecutive isolates distinguished reinfection from recurrence and contributed to the diagnosis of a factitious disorder.

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