scholarly journals Identification of a Recently Dominant Sublineage in Salmonella 4,[5],12:i:- Sequence Type 34 Isolated From Food Animals in Japan

2021 ◽  
Vol 12 ◽  
Author(s):  
Nobuo Arai ◽  
Tsuyoshi Sekizuka ◽  
Yukino Tamamura-Andoh ◽  
Lisa Barco ◽  
Atsushi Hinenoya ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Mobile Genetic Element ◽  
Sequence Type ◽  
Whole Genome ◽  
Phase 2 ◽  
Genetic Element ◽  
Gene Encoding ◽  
Antimicrobial Resistance Genes ◽  
Serovar Typhimurium ◽  
Food Animals

Salmonella enterica subsp. enterica serovar Typhimurium sequence type 34 (ST34) and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most frequently isolated clones from both humans and animals worldwide. Our previous study demonstrated that Salmonella Typhimurium/4,[5],12:i:- strains isolated in Japan could be classified into nine clades and that clade 9 consisted of ST34 strains. In Japan, ST34/clade 9 was first found in the 1990s and has become predominant among food animals in recent years. In the present study, we analyzed the whole genome-based phylogenetic relationships and temporal information of 214 Salmonella Typhimurium/4,[5],12:i:- ST34/clade 9 strains isolated from 1998 to 2017 in Japan. The 214 strains were classified into two sublineages: the newly identified clade 9–2 diverged from clade 9 in the early 2000s and has predominated in recent years. Clonally expanding subclades in clades 9–1 or 9–2 lacked Gifsy-1 or HP1 prophages, respectively, and some strains in these subclades acquired plasmids encoding antimicrobial resistance genes. Additional genome reduction around the fljB gene encoding the phase 2-H antigen was generated by an IS26-mediated deletion adjacent to the transposon in clade 9–2. Although most of the clade 9 strains were isolated from cattle in Japan, the clonally expanding subclades in clade 9–2 (i.e., all and 24% strains of subclades 9–2a and 9–2b, respectively) were isolated from swine. The spread of clade 9 in recent years among food animals in Japan was responsible for the emergence of multiple host-adapted sublineages involving the clonally expanding subclades generated by mobile genetic element-mediated microevolution.

scholarly journals Identification of a recently dominate sublineage in Salmonella 4,[5],12:i:- sequence type 34 isolated from food animals in Japan

2020 ◽  
Author(s):  
Nobuo Arai ◽  
Tsuyoshi Sekizuka ◽  
Yukino Tamamura-Andoh ◽  
Lisa Barco ◽  
Atsushi Hinenoya ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Phylogenetic Relationships ◽  
Mobile Genetic Element ◽  
Sequence Type ◽  
Whole Genome ◽  
Genetic Element ◽  
Food Animals

AbstractSalmonella Typhimurium and its monophasic variant (Salmonella 4,[5],12:i:-) are classified into nine clades. Clade 9 is composed of ST34 strains, including the Salmonella 4,[5],12:i:-European clone, which has rapidly disseminated in humans and animals worldwide since the 2000s. To reveal the microevolution of ST34/clade 9, we analyzed the whole-genome-based phylogenetic relationships of 230 Salmonella Typhimurium and Salmonella 4,[5],12:i:-strains isolated between 1998 and 2017 in Japan and other countries. We identified clade 9-2, a novel sublineage derived from the conventional Salmonella 4,[5],12:i:-clade 9 that exclusively consists of Japanese isolates. Clade 9-2 was generated by mobile genetic element-mediated stepwise genome reductions caused by IS26 and prophages. Furthermore, the recently identified strains developed further resistance to antimicrobials via the acquisition of resistance genes. During this microevolution, Salmonella 4,[5],12:i:-clade 9-2 has dominated among recent isolates from food animals in Japan via the emergence of clonally expanding and/or multiple host-adapted subclades.

scholarly journals Draft Whole-Genome Sequences of Two Multidrug-Resistant Salmonella enterica Serovar Senftenberg Sequence Type 14 Strains Resistant to Ciprofloxacin, Ceftriaxone, and/or Azithromycin, Isolated from Kolkata, India

2022 ◽  
Author(s):  
Priyanka Jain ◽  
Rajlakshmi Viswanathan ◽  
Gourab Halder ◽  
Sulagna Basu ◽  
Shanta Dutta
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Goat Meat ◽  
Antimicrobial Resistance Genes

We report draft whole-genome sequences of two multidrug-resistant Salmonella enterica serovar Senftenberg sequence type 14 strains resistant to ciprofloxacin, ceftriaxone, and/or azithromycin, which were isolated from neonatal stool and goat meat in Kolkata, India. The genome characteristics, as well as the antimicrobial resistance genes, plasmid types, and integrons, are presented in this report.

scholarly journals ICEHpsaHPS7, a novel multiple drug-resistance integrative conjugative element in Glaesserella parasuis

2020 ◽  
Author(s):  
Jiahui An ◽  
Genglin Guo ◽  
Dong Yu ◽  
Kexin Zhu ◽  
Chao Zhang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Antimicrobial Resistance ◽  
Mobile Genetic Element ◽  
Multiple Drug Resistance ◽  
Multiple Drug ◽  
Haemophilus Parasuis ◽  
Genetic Element ◽  
Integrative Conjugative Element ◽  
Antimicrobial Resistance Genes ◽  
Integrative Conjugative Elements

Integrative conjugative elements (ICEs), a kind of novel self-transmissible mobile genetic element. In this study, a novel ICE was identified in Glaesserella (Haemophilus) parasuis. We confirmed that it could mediate the migration of antimicrobial resistance genes in G. parasuis and found that there may have been a transferring potential between different serovar strains of G. parasuis. These findings demonstrate that ICE is crucial to the horizontal transfer of antimicrobial resistance among G. parasuis.

scholarly journals Detection of colistin resistance mcr-1 gene in Salmonella enterica serovar Rissen isolated from mussels, Spain, 2012­ to 2016

2019 ◽  
Vol 24 (16) ◽  
Author(s):  
Antonio Lozano-Leon ◽  
Carlos Garcia-Omil ◽  
Jacobo Dalama ◽  
Rafael Rodriguez-Souto ◽  
Jaime Martinez-Urtaza ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Salmonella Enterica ◽  
Sequence Type ◽  
Monitoring Programme ◽  
Colistin Resistance ◽  
North West ◽  
Antimicrobial Resistance Genes

Nineteen Salmonella strains were isolated from 5,907 randomly selected mussel samples during a monitoring programme for the presence of Salmonella in shellfish in Galicia, north-west Spain (2012–16). Serovars, sequence type and antimicrobial resistance genes were determined through genome sequencing. Presence of the mcr-1 gene in one strain belonging to serovar Rissen and ST-469 was identified. The mcr-1 gene had not been isolated previously in environmental Salmonella isolated from mussels in Spain.

scholarly journals Multidrug-Resistant Streptococcus agalactiae Strains Found in Human and Fish with High Penicillin and Cefotaxime Non-Susceptibilities

2020 ◽  
Vol 8 (7) ◽  
pp. 1055
Author(s):  
Carmen Li ◽  
Dulmini Nanayakkara Sapugahawatte ◽  
Ying Yang ◽  
Kam Tak Wong ◽  
Norman Wai Sing Lo ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Streptococcus Agalactiae ◽  
Novel Mutation ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Healthcare Facilities ◽  
Surveillance Studies ◽  
Penicillin Binding Proteins ◽  
Antimicrobial Resistance Genes

Penicillin non-susceptible Streptococcus agalactiae (PEN-NS GBS) has been increasingly reported, with multidrug-resistant (MDR) GBS documented in Japan. Here we identified two PEN-NS GBS strains during our surveillance studies: one from a patient’s wound and the other from a tilapia. The patient’s GBS (H21) and fish GBS (F49) were serotyped and tested for antibiotic susceptibility. Whole-genome sequencing was performed to find the sequence type, antimicrobial resistance genes, and mutations in penicillin-binding proteins (PBPs) and fluoroquinolone (FQ) resistance genes. H21 and F49 belonged to ST651, serotype Ib, and ST7, serotype Ia, respectively. H21 showed PEN and cefotaxime minimum inhibitory concentrations (MICs) of 2.0 mg/L. F49 showed PEN MIC 0.5 mg/L. H21 was MDR with ermB, lnuB, tetS, ant6-Ia, sat4a, and aph3-III antimicrobial resistance genes observed. Alignment of PBPs showed the combination of PBP1B (A95D) and 2B mutations (V80A, S147A, S160A) in H21 and a novel mutation in F49 at N192S in PBP2B. Alignment of FQ-resistant determinants revealed mutation sites on gyrA, gyrB, and parC and E in H21. To our knowledge, this is the first report of GBS isolates with such high penicillin and cefotaxime MICs. This raises the concern of emergence of MDR and PEN-NS GBS in and beyond healthcare facilities.

scholarly journals Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades

2020 ◽  
Vol 11 ◽  
Author(s):  
Grazielle Lima Rodrigues ◽  
Pedro Panzenhagen ◽  
Rafaela Gomes Ferrari ◽  
Anamaria dos Santos ◽  
Vania Margaret Flosi Paschoalin ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
In Silico ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Antimicrobial Resistance Genes

scholarly journals Emergence of mosaic plasmids harboring Tn1546-ermBelement inStaphylococcus aureusisolates

2018 ◽  
Author(s):  
Tsai-Wen Wan ◽  
Yu-Tzu Lin ◽  
Wei-Chun Hung ◽  
Jui-Chang Tsai ◽  
Yu-Jung Liu ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Continuous Monitoring ◽  
Mobile Genetic Element ◽  
Clonal Complex ◽  
Genetic Element ◽  
Novel Structure ◽  
Important Means ◽  
Sequence Types

ABSTRACTAntimicrobial resistance inStaphylococcus aureusis a major problem and the acquisition of resistance genes may occur by horizontal gene transfer (HGT). The transposon, an important means of HGT, is recognized as a mobile genetic element that can integrate in plasmids, replicate and transfer to other strains. We have previously reported a novel structure of theEnterococcus faecium-originated Tn1546-ermBelement inS. aureus. The emergence of the Tn1546-like element is an emerging problem that requires continuous monitoring. In the present study, we expand the examination of Tn1546-ermBelement toermB-positive methicillin-susceptibleS. aureus(MSSA) (n = 116) andermB-positive methicillin-resistantS. aureus(MRSA) (n = 253) during a 16-year period, from 2000 to 2015. PCR mapping showed that 10 MSSA and 10 MRSA carried the Tn1546-ermBelement. The 10 MSSA belonged to three sequence types (ST), ST7 (n = 6), ST5 (n = 3), and ST59 (n = 1), and the 10 MRSA belonged to two STs, ST188 (n = 8) and ST965 (n = 2). Since only clonal complex 5 (including ST5, ST85, ST231, and ST371) MRSA, ST8 MRSA and ST5 MSSA have been previously reported to carry Tn1546plasmids, this is the first report describing the presence of the Tn1546-ermBelement in ST7/5/59 MSSA and ST188/965 MRSA. Plasmid sequencing revealed that the Tn1546-ermBelement was harbored by five different mosaic plasmids. In addition to resistance genes, some plasmids also harbored toxin genes.

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