J E Coia

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.

Sourcing Antibiotic Resistance It is widely assumed that antibiotic resistance in farm animals contributes in a major way to antibiotic resistance in humans. Mather et al. (p. 1514, published online 12 September; see the Perspective by Woolhouse and Ward) analyzed hundreds of genome sequences from Salmonella isolates collected from both livestock and patients in Scotland between 1990 and 2004. The relative contributions of animal-derived and human-derived sources of infection were quantified and the phylogenetic diversity of resistance profiles was matched with bacterial phylogenies. The results suggest that most human infections are caught from other humans rather than from livestock and that humans harbor a greater diversity of antibiotic resistance. Antibiotic resistance travels in independent epidemics in humans and their livestock. [Also see Perspective by Woolhouse and Ward] The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.

Comparison of enterotoxins and haemolysins produced by methicillin-resistant (MRSA) and sensitive (MSSA) Staphylococcus aureus

A collection of 201 isolates of Staphylococcus aureus was examined: 152 methicillin-sensitive S. aureus (MSSA) comprised 48 blood culture isolates (BC) and 58 isolates from routine diagnostic specimens (RD) from Glasgow Royal Infirmary (GRI), and 46 strains from nasal swabs of patients attending a general practitioner (GP); 49 isolates were of methicillin-resistant S. aureus (MRSA) from GRI. We have previously shown that the MRSA could be divided into two sub-groups on the basis of sensitivity or resistance to aminoglycoside antibiotics. Production of enterotoxins A, B, C and D, and alpha-, beta-, gamma- and delta- haemolysins was detected by reverse passive latex agglutination (RPLA) and agar overlay methods respectively: 60% of BC MSSA and a similar proportion of MSSA from other sources produced enterotoxin; 87% of aminoglycoside-sensitive MRSA produced enterotoxin (89% of these produced enterotoxin A alone) whereas only 27% of aminoglycoside-resistant MRSA were enterotoxin-positive, significantly less than either MSSA or aminoglycoside-sensitive MRSA. The proportion of haemolysin-producing isolates did not differ amongst the isolates of MSSA and MRSA; there was no difference in the distributions of haemolysins between aminoglycoside-sensitive and -resistant strains of MRSA. GP MSSA had higher and lower numbers of gamma- and delta-haemolysin producers respectively than other S. aureus isolates. alpha-Haemolysin producers were commoner amongst MRSA isolates, which were also more likely than MSSA isolates to produce several haemolysins. Differences in enterotoxin production between aminoglycoside-sensitive and -resistant MRSA isolates reflect subgroups previously defined by biotype, phage type, immunoblot and restriction enzyme fragmentation pattern data, and provide further evidence for the existence of two major MRSA clones in GRI.

What is the role of antimicrobial resistance in the new epidemic of Clostridium difficile

The epidemiology of Clostridium difficile infection (CDI) has changed in recent years, with the occurrence of large outbreaks of infection associated with the emergence of hypervirulent strains, particularly PCR ribotype 027. There has been much speculation as to the nature of the factors responsible for driving the new epidemic of CDI, and various hypotheses have been proposed. These include increases in the size of the population at risk of CDI and/or their susceptibility to infection, increased exposure to the organism, and changes in the virulence/ transmissibility of the pathogen. Resistance to a range of antimicrobial agents, including the fluoroquinolones, is a common feature of these newly emerged strains. This article considers the part antimicrobial resistance may play as a driver for the observed changes in the epidemiology of CDI and presents a model that would support such a role. However, the paucity of definitive evidence for a causal role and the complexity of the epidemiology of CDI are acknowledged. It may be more accurate to view antimicrobial resistance as one of a range of factors which interact to alter the parameters of the CDI equation, and thereby determine the size of the CDI problem associated with any given emerging subtype of C. difficile.

Plasmid-mediated quinolone resistance in nalidixic-acid-susceptible strains of Salmonella enterica isolated in Scotland

Sir, Chromosomal mutations in the topoisomerase II gene gyrA and altered drug accumulation were considered to be the only mechanisms of quinolone resistance until 1998, when the plasmidmediated quinolone resistance gene, qnrA, was described in an isolate of Klebsiella pneumoniae. Since then, other plasmidborne resistance genes, qnrB, qnrS (and their variants), aac(60)-Ib-cr and qepA, have been identified. The clinical importance of these qnr genes is that, although not conferring detectable resistance according to the criteria set by the CLSI or BSAC (currently 4 mg/L for ciprofloxacin), their presence facilitates the recovery of mutants with elevated levels of resistance to quinolones. The presence of qnr has frequently been detected in strains producing extended-spectrum b-lactamases (ESBLs). We investigated a total of 70 isolates of Salmonella enterica that were selected based on reduced susceptibility to ciprofloxacin ( 0.125 mg/L) for the presence of qnr genes. Duplicate samples were excluded, and only a single representative isolate from each outbreak was included. Of these 70 isolates, 53 were susceptible to nalidixic acid (,40 mg/L). The remaining 17 isolates exhibited additional resistance to cefotaxime (1 mg/L). Antimicrobial resistances were determined using an in-house breakpoint method. Isolates were screened for qnr genes by a touchdown multiplex PCR using primers described previously. Transconjugants of Escherichia coli J53 harbouring plasmids pMG252, pMG298 and pMG306 were used as positive controls for qnrA1, qnrB1 and qnrS1, respectively. The results of the study are summarized in Table 1. Of the 34 isolates positive for one of the qnr genes, 30 were of human origin; the remaining 4 were isolated from ovine (2), bovine (1) and environmental (1) sources. qnr genes were identified in 12 different serotypes. Salmonella Corvallis was the most common with 13 strains accounting for 38%, followed by 9 Salmonella Typhimurium (26%) and 2 each of Salmonella Stanley and Salmonella Enteritidis (6%). The remaining eight serotypes, Salmonella Virchow, Salmonella Haifa, Salmonella Agona, Salmonella Gaminara, Salmonella Blockley, Salmonella Rissen, Salmonella Colindale and a monophasic strain of Salmonella Java, were each represented by a single strain (3%). qnrA1 was identified in strains of Salmonella Virchow and Salmonella Stanley. qnrB1 was identified in Salmonella Colindale, with qnrB2 being identified in Salmonella Agona and Salmonella Haifa. qnrB5 was identified in Salmonella Gaminara. With the exception of these six strains, all other qnr genes were identified as qnrS1. These results are similar to those of other laboratories. Scientists in Denmark identified qnrS1 in every one of the 23 strains of Salmonella Corvallis they examined, while scientists in England identified the qnrS1 gene in all but 2 of the 39 isolates confirmed as carrying the qnr genes. Of the 18 strains isolated from patients with a history of foreign travel, 16 were identified as harbouring qnrS1, one, qnrA1 and another, qnrB2. With the exception of two strains from South America and Africa, all qnrS1-positive strains originated from the Far East. Reports on the identification of qnr genes have been increasingly frequent around the world; however, this is the first report of their presence in strains of Salmonella isolated in Scotland. The 34 qnr-positive strains belonged to 12 serotypes, including Salmonella Gaminara, Salmonella Rissen, Salmonella Agona, Salmonella Haifa, Salmonella Blockley, Salmonella Colindale and a monophasic strain of Salmonella Java. To the best of our knowledge, there have been no previous reports of the identification of qnr genes in these serotypes. Plasmid-mediated quinolone resistance has serious implications for the use of this group of antimicrobials in the future. More importantly, the presence of these genes on integrons together with ESBLs further supports the necessity for ongoing surveillance of resistance. Surveillance will be problematic, in that routine diagnostic laboratories rarely test for reduced susceptibility to fluoroquinolones. This problem was addressed by the recommendation that nalidixic acid disc screening was indicative of fluoroquinolone susceptibility. However, as this study has shown, isolates that are nalidixic-acid-susceptible can possess qnr genes and have an MIC of ciprofloxacin as high as 0.75 mg/L. However, two cefotaxime-resistant strains with an MIC of ciprofloxacin of 1 mg/L were cross-resistant to nalidixic acid. The elevated MIC may indicate the presence of gyrase mutations in these strains and warrants further investigation. Although these strains are not considered resistant by CLSI or BSAC criteria, elevated MICs of ciprofloxacin have been shown to contribute to treatment failures in the past. This new mechanism of reduced susceptibility in Enterobacteriaceae again raises the question of the appropriateness of the current breakpoints for fluoroquinolones.

Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis.

Since April 2015, whole genome sequencing (WGS) has been the routine test for Salmonella identification, surveillance and outbreak investigation at the national reference laboratory in England and Wales. In May 2015, an outbreak of Salmonella Enteritidis cases was detected using WGS data and investigated. UK cases were interviewed to obtain a food history and links between suppliers were mapped to produce a food chain network for chicken eggs. The association between the food chain network and the phylogeny was explored using a network comparison approach. Food and environmental samples were taken from premises linked to cases and tested for Salmonella. Within the outbreak single nucleotide polymorphism defined cluster, 136 cases were identified in the UK and 18 in Spain. One isolate from a food containing chicken eggs was within the outbreak cluster. There was a significant association between the chicken egg food chain of UK cases and phylogeny of outbreak isolates. This is the first published Salmonella outbreak to be prospectively detected using WGS. This outbreak in the UK was linked with contemporaneous cases in Spain by WGS. We conclude that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.

The epidemiology of Clostridium difficile in Scotland

The objective of this study was to characterise the epidemiology of Clostridium difficile in Scotland by determining the distribution of PCR ribotypes and antimicrobial susceptibility in 1613 isolates collected from all healthboard areas of Scotland in the period November 2007-December 2009. Three PCR ribotypes predominated amongst the Scottish isolates of C. difficile; ribotype 106 (29.4%), ribotype 001 (22%) and ribotype 027 (12.6%) followed by the less prevalent ribotypes including 002, 015, 014, 078, 005, 023 and 020. The distribution of ribotypes varied between healthboard areas. Ribotype 106 or 001 was the predominant ribotype in 10 healthboard areas, while ribotype 027 was the predominant type in two neighbouring areas. Antimicrobial susceptibility testing of C. difficile isolates showed high frequencies of resistance to moxifloxacin, levofloxacin, erythromycin and cefotaxime in the epidemic C. difficile ribotypes 001, 027 and 106 compared to other less common ribotypes. Furthermore, reduced susceptibility to metronidazole was found only in the epidemic strains. These findings are compatible with the hypothesis that fluoroquinolones, macrolides and cephalosporins may play a role in the spread of C. difficile in Scotland (while the role of metronidazole needs further investigations), and highlights the role of antimicrobial stewardship in preventing and controlling C. difficile infection (CDI).

Isolation of avian strains of Salmonella enterica serovar Typhimurium from cats with enteric disease in the United Kingdom

AVIAN-ADAPTED strains of Salmonella enterica serovar Typhimurium have been detected in wild birds, particularly finches (family Fringillidae), in Europe, Scandinavia and North America ([Daoust and others 2000][1], [Tauni and Osterlund 2000][2], [Pennycott and others 2006][3]). In the uk, these

The Prevalences of Salmonella Genomic Island 1 Variants in Human and Animal Salmonella Typhimurium DT104 Are Distinguishable Using a Bayesian Approach

Throughout the 1990 s, there was an epidemic of multidrug resistant Salmonella Typhimurium DT104 in both animals and humans in Scotland. The use of antimicrobials in agriculture is often cited as a major source of antimicrobial resistance in pathogenic bacteria of humans, suggesting that DT104 in animals and humans should demonstrate similar prevalences of resistance determinants. Until very recently, only the application of molecular methods would allow such a comparison and our understanding has been hindered by the fact that surveillance data are primarily phenotypic in nature. Here, using large scale surveillance datasets and a novel Bayesian approach, we infer and compare the prevalence of Salmonella Genomic Island 1 (SGI1), SGI1 variants, and resistance determinants independent of SGI1 in animal and human DT104 isolates from such phenotypic data. We demonstrate differences in the prevalences of SGI1, SGI1-B, SGI1-C, absence of SGI1, and tetracycline resistance determinants independent of SGI1 between these human and animal populations, a finding that challenges established tenets that DT104 in domestic animals and humans are from the same well-mixed microbial population.