New Variant of Multidrug-Resistant
            <i>Salmonella enterica</i>
            Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam

Mather, Alison E.; Phuong, Tu Le Thi; Gao, Yunfeng; Clare, Simon; Mukhopadhyay, Subhankar; Goulding, David; Hoang, Nhu Tran Do; Tuyen, Ha Thanh; Lan, Nguyen Phu Huong; Thompson, Corinne N.; Trang, Nguyen Hoang Thu; Carrique-Mas, Juan; Tue, Ngo Tri; Campbell, James I.; Rabaa, Maia A.; Thanh, Duy Pham; Harcourt, Katherine; Hoa, Ngô Thị; Trung, Nguyen Vinh; Schultsz, Constance; Perron, Gabriel G.; Coia, John; Brown, D. J. F.; Okoro, Chinyere K.; Parkhill, Julian; Thomson, Nicholas R.; Châu, Nguyễn Văn Vĩnh; Thwaites, Guy; Maskell, Duncan J.; Dougan, Gordon; Kenney, Linda J.; Baker, Stephen

doi:10.1128/mbio.01056-18

Cited by 62 publications

(97 citation statements)

References 39 publications

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“…Indeed some β subclades such as those associated with the DT56, DT2 and DT8 complexes that are well characterized host adapted clonal groups 11,12,21 , contained exclusively isolates from avian species, and were present on relatively extended internal branches. This general phylogenetic topology is consistent with that described for distinct collections of S. Typhimurium strains from North America and Asia 36,37 .…”

Section: Discussionsupporting

confidence: 88%

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

Bawn

Thilliez

Kirkwood

et al. 2019

Preprint

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Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and disseminated disease worldwide, and a model organism for host pathogen interactions. Genotypic variation of S. Typhimurium results in strains with diverse host range, pathogenicity and risk to food safety. A robust fully parsimonious phylogenetic tree constructed from recombination purged variation in the whole genome sequence of 131 diverse strains of S. Typhimurium revealed population structure composed of two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β predominantly contained subclades associated with wild avian species, with the notable exception of a subclade containing the DT204/49 complex. The contrasting epidemiology of α and β strains was reflected in distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification associated with invasiveness of host adapted serotypes. Gene flux was predominantly driven by acquisition, loss or recombination of prophage, awhile acquisition of large genetic islands (SGI-1 and 4) was restricted to two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) in clade α.Together, our data are consistent with the view that a broad host range common ancestor of S.Typhimurium diversified with clade α lineages remained largely associated with multiple domesticated animal species, while clade β spawned multiple lineages that underwent diversifying selection associated with adaptation to various niches, predominantly in wild avian species.

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Section: Discussionsupporting

confidence: 88%

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

Bawn

Thilliez

Kirkwood

et al. 2019

Preprint

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“…The most invasive serovars from England (S. Poona, S. Panama, and S. Dublin) have also been noted in other developed countries, like the United States and Australia (4,26). We found that S. Typhimurium was not the most invasive serovar in England, which is very different from other countries and regions, such as Australia, South East Asia, and sub-Saharan Africa, where invasive S. Typhimurium predominates (26)(27)(28).…”

Section: Discussioncontrasting

confidence: 49%

Epidemiology and Outcomes of Nontyphoidal Salmonella Bacteremias from England, 2004 to 2015

et al. 2019

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Nontyphoidal Salmonella (NTS) bacteremia causes hospitalization and high morbidity and mortality. We linked Gastrointestinal Bacteria Reference Unit (GBRU) data to the Hospital Episode Statistics (HES) data set to study the trends and outcomes of NTS bacteremias in England between 2004 and 2015. All confirmed NTS isolates from blood from England submitted to GBRU between 1 January 2004 and 31 December 2015 were deterministically linked to HES records. Adjusted odds ratios (AOR), proportions, and confidence intervals (CI) were calculated to describe differences in age, sex, antibiotic resistance patterns, and serotypes over time. Males, neonates, and adults above 65 years were more likely to have NTS bacteremia (AOR, 1.54 [95% CI, 1.46 to 1.67]; 2.57 [95% CI, 1.43 to 4.60]; and 3.56 [95% CI, 3.25 to 3.90], respectively). Proportions of bacteremia increased from 1.41% in 2004 to 2.67% in 2015. Thirty-four percent of all blood isolates were resistant to a first-line antibiotic, and 1,397 (56%) blood isolates were linked to an HES record. Of the patients with NTS bacteremia, 969 (69%) had a cardiovascular condition and 155 (12%) patients died, out of which 120 (77%) patients were age 65 years and above. NTS bacteremia mainly affects older people with comorbidities placing them at increased risk of prolonged hospital stay and death. Resistance of invasive NTS to first-line antimicrobial agents appeared to be stable in England, but the emergence of resistance to last-resort antibiotics, such as colistin, requires careful monitoring.

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“…During the past decade, blaCTX-M-55 has been increasingly found in Enterobacteriaceae isolated from humans, animals, and the environment (36). Recently, mcr genes were found in Salmonella Typhimurium/4, [5],12:i:-ST34 isolated from humans and swine in North America, Europe, Australia, and Asian countries other than Japan (8,11,34,37,38). The present study is the first to identify mcr-1, mcr-3, mcr-5, and/or mcr-9 in Salmonella 4, [5],12:i:-ST34 disseminated into food animals in Japan.…”

Section: Acquisition Of Amr In Clade 9 Strainsmentioning

confidence: 99%

“…Salmonella 4, [5],12:i:-infections have been increasingly occurring in European countries since the 2000s and have since spread to the United States, South America, Australia, and Asia (3)(4)(5)(6)(7)(8)(9). A European clone is one of the best studied Salmonella 4, [5],12:i:isolates because of its rapid and worldwide dissemination (6,(9)(10)(11). Swine was reported as the main reservoir of this clone, and the contaminated products are considered causative agents of food-borne infection (12).…”

Section: Introductionmentioning

confidence: 99%

“…The acquisition of resistance to clinically important antimicrobials is a well-studied factor regarding the clonal expansion of bacterial strains (18). Several studies have reported the acquisition of antimicrobial resistance (AMR) in addition to core antimicrobials in Salmonella 4, [5],12:i-ST34; the recent swine isolates acquired trimethoprim and/or gentamycin resistance via plasmids in the United Kingdom (19), and human isolates possessed a large IncHI2 plasmid (246 kb) carrying multiple AMR genes in Vietnam (11). MGEs are known to play an important role in the transmission of various genes, but the factors underlying the acquisition of such large plasmids by recently isolated ST34 strains have not been fully elucidated.…”

Section: Introductionmentioning

confidence: 99%

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Identification of a recently dominate sublineage inSalmonella4,[5],12:i:- sequence type 34 isolated from food animals in Japan

Arai

Sekizuka

Tamamura-Andoh

et al. 2020

Preprint

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Salmonella 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.

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New Variant of Multidrug-Resistant Salmonella enterica Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam

Cited by 62 publications

References 39 publications

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

Epidemiology and Outcomes of Nontyphoidal Salmonella Bacteremias from England, 2004 to 2015

Identification of a recently dominate sublineage inSalmonella4,[5],12:i:- sequence type 34 isolated from food animals in Japan

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