Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.

Liljana Petrovska,Julian Parkhill,Robert A Kingsley,Thomas Connor,Gordon Dougan,Andrew Page,John Wain,K.L Hopkins,Alison E Mather,Antonia A Lettini,A Underwood,Simon R Harris,Manal Abuoun,Mary Bagnall,Robert Davies,Priscilla Branchu

doi:10.3201/eid2204.150531

Abstract

Microevolution associated with emergence and expansion of new epidemic clones of bacterial pathogens holds the key to epidemiologic success. To determine microevolution associated with monophasic Salmonella Typhimurium during an epidemic, we performed comparative whole-genome sequencing and phylogenomic analysis of isolates from the United Kingdom and Italy during 2005-2012. These isolates formed a single clade distinct from recent monophasic epidemic clones previously described from North America and Spain. The UK monophasic epidemic clones showed a novel genomic island encoding resistance to heavy metals and a composite transposon encoding antimicrobial drug resistance genes not present in other Salmonella Typhimurium isolates, which may have contributed to epidemiologic success. A remarkable amount of genotypic variation accumulated during clonal expansion that occurred during the epidemic, including multiple independent acquisitions of a novel prophage carrying the sopE gene and multiple deletion events affecting the phase II flagellin locus. This high level of microevolution may affect antigenicity, pathogenicity, and transmission.

Highlights

Microevolution associated with emergence and expansion of new epidemic clones of bacterial pathogens holds the key to epidemiologic success
The first description of a monophasic Salmonella Typhimurium epidemic in Europe was that of a “Spanish clone,” which emerged rapidly during 1997 and was characterized by a deletion in the allantoin–glyoxylate operon and the fljAB operon, phage type U302, and resistance pattern ACSuGSTSxT (10)
In contrast to the Spanish clone, these current monophasic Salmonella Typhimurium epidemic strains have commonly been associated with phage types DT193 or DT120 and a predominant

Summary

Introduction

Microevolution associated with emergence and expansion of new epidemic clones of bacterial pathogens holds the key to epidemiologic success. The first description of a monophasic Salmonella Typhimurium epidemic in Europe was that of a “Spanish clone,” which emerged rapidly during 1997 and was characterized by a deletion in the allantoin–glyoxylate operon and the fljAB operon, phage type U302, and resistance pattern ACSuGSTSxT (resistant to ampicillin, chloramphenicol, sulfonamide, gentamicin, streptomycin, tetracycline, and co-trimoxazole) (10). Since this time, many European countries have reported increased incidence of this serotype, associated with pig herds (12–15) but later with cattle (16,17). The current multidrug-resistant Salmonella 4,[5],12:i:- epidemic in the Europe was first reported around 2005 and is mainly associated with isolates of phage types DT193 and DT120 (18)

Methods

Results

Conclusion