Thursday, April 4, 2013

Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC

Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC




Ewan M. Harrison1, Gavin K. Paterson1, Matthew T.G. Holden2, Jesper Larsen3, Marc Stegger3, Anders Rhod Larsen3, Andreas Petersen3, Robert L. Skov3, Judit Marta Christensen4, Anne Bak Zeuthen4, Ole Heltberg4, Simon R. Harris2, Ruth N. Zadoks5, Julian Parkhill2, Sharon J. Peacock2,6, Mark A. Holmes1*




Keywords: cattle; mecC; MRSA; sheep; zoonosis




DOI 10.1002/emmm.201202413 Received December 21, 2012 Revised February 06, 2013 Accepted February 08, 2013 GSee accompanying article http://dx.doi.org/10.1002/emmm.201302622





Several methicillin-resistant Staphylococcus aureus (MRSA) lineages that carry a novel mecA homologue (mecC) have recently been described in livestock and humans. In Denmark, two independent human cases of mecC-MRSA infection have been linked to a livestock reservoir. We investigated the molecular epidemiology of the associated MRSA isolates using whole genome sequencing (WGS). Single nucleotide polymorphisms (SNP) were defined and compared to a reference genome to place the isolates into a phylogenetic context. Phylogenetic analysis revealed two distinct farm-specific clusters comprising isolates from the human case and their own livestock, whereas human and animal isolates from the same farm only differed by a small number of SNPs, which supports the likelihood of zoonotic transmission. Further analyses identified a number of genes and mutations that may be associated with host interaction and virulence. This study demonstrates that mecC-MRSA ST130 isolates are capable of transmission between animals and humans, and underscores the potential of WGS in epidemiological investigations and source tracking of bacterial infections.





The paper explained




PROBLEM:




The emergence of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) is a major public health concern. Recently, MRSA strains with a novel mecA homologue (mecC), which may go undetected by current diagnostic tests, were described in both livestock and humans suggesting potential zoonotic transmission. Denmark has reported a significant increase in cases of CC130 mecC-MRSA between 2003 and 2011 and two independent human cases of mecC-MRSA infection directly linked to a livestock reservoir have been identified.




RESULTS:




We investigated the molecular epidemiology of these livestockassociated mecC-MRSA cases using WGS. Phylogenetic analysis across the entire core genome revealed that the isolates from these cases form two distinct, farm-specific clusters comprising near identical isolates from the human case and from livestock on that farm. Within each cluster, the human and animal isolates only differed by a small number of SNPs, which supports the premise of zoonotic transmission. In-depth genome analysis identified a number of candidate genes and mutations that may be associated with host–pathogen interactions and virulence of this emerging MRSA clone.




IMPACT:




Our findings demonstrate that the CC130 MRSA lineage is capable of transmission between animals and humans, further highlighting the role of livestock as a reservoir for MRSA. Our study also underscores the potential of WGS in epidemiological investigations and source tracking of bacterial infections.















TSS

Wednesday, January 2, 2013

New MRSA ST398 superbug strain found in UK milk Occupational risk factor

Rapid communications



First detection of livestock-associated meticillinresistant Staphylococcus aureus CC398 in bulk tank milk in the United Kingdom, January to July 2012



G K Paterson1, J Larsen2, E M Harrison1, A R Larsen2, F J Morgan1, S J Peacock3,4, J Parkhill4, R N Zadoks5, M A Holmes (mah1@cam.ac.uk)1


1. Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom


2. Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark


3. School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom


4. The Wellcome Trust Sanger Institute, Wellcome Trust, Cambridge, United Kingdom


5. Moredun Research Institute, Penicuik, United Kingdom



Citation style for this article:



Paterson GK, Larsen J, Harrison EM, Larsen AR, Morgan FJ, Peacock SJ, Parkhill J, Zadoks RN, Holmes MA. First detection of livestock-associated meticillin-resistant Staphylococcus aureus CC398 in bulk tank milk in the United Kingdom, January to July 2012. Euro Surveill. 2012;17(50):pii=20337. Available online: http://www. eurosurveillance.org/ViewArticle.aspx?ArticleId=20337



Article submitted on 27 November 2012 / published on 13 December 2012




Livestock-associated meticillin-resistant Staphylococcus aureus belonging to clonal complex 398 (LA-MRSA CC398) is an important cause of zoonotic infections in several countries, but there is only a single published report of this lineage from the United Kingdom (UK). Here, we describe the isolation of LA-MRSA CC398 from bulk tank milk from five geographically dispersed farms in the UK. Our findings suggest that LA-MRSA CC398 is established in livestock in the UK. Awareness of the potential occupational risks and surveillance in other food-producing animal species should be promoted.





Isolation of meticillin-resistant Staphylococcus aureus from dairy cattle




During a study, performed from January to July 2012, to detect mecC meticillin-resistant Staphylococcus aureus (MRSA) in dairy cattle in the United Kingdom (UK), ca. 1,500 bulk tank milk samples were supplied by National Milk Laboratories Ltd., (Chippenham, UK). These were collected aseptically by trained technicians for quality assurance purposes and stored at 4 °C for up to five days prior to testing. Enrichment for S. aureus was performed using a modification of a published technique [1] omitting the incubation in phenol red mannitol broth supplemented with 4 mg/L oxacillin (24 h at 37°C). Identification of potential MRSA colonies (blue colour) was confirmed by subculture on Staph Brilliance 24 plates (Oxoid, Baskingstoke, UK) and these were subsequently screened for mecA, mecC and femB by multiplex PCR as described previously [2]. Approximately 300 potential MRSA colonies were identified and subjected to PCR testing, yielding a total of seven mecA MRSA isolates from five farms, including three isolates from the same farm. These isolates were found to be mecA, femB-positive by PCR (Table). All seven isolates were resistant to penicillin, meticillin and cefoxitin by disk diffusion according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines [3].




Molecular and phenotypic characterisation of LA-MRSA CC398 from dairy cattle in the United Kingdom




Multi-locus sequence typing found all seven isolates belonged to sequence type ST398, and CC398-specific PCR based on the restriction–modification system sau1–hsdS1 confirmed that all the isolates belonged to clonal complex CC398 [4]. Isolates from three farms exhibited spa type t011 and carried a composite staphylococcal cassette chromosome mec (SCCmec) V(5C2&5)c element, whereas isolates from the remaining two farms had spa types t011 and t2546 and harboured SCCmec IVa. All isolates lacked the lukS-PV and lukF-PV genes encoding Panton-Valentine leukocidin and the scn gene (Table). Antimicrobial susceptibility testing using disk diffusion according to the EUCAST guidelines revealed that all isolates were resistant to tetracycline, and PCR [10] demonstrated the presence of the tetracycline resistance gene tet(M) in all seven, and of tet(K) in three isolates (Table).




Discussion




Here we describe the first isolation of LA-MRSA CC398 from dairy cattle in the UK. This is only the second published instance of LA-MRSA CC398 in this country following the report of isolates (t011 and SCCmec IVa) from two horses in south-eastern England [11]. In many countries in continental Europe and elsewhere, LA-MRSA CC398 poses an occupational risk for those in close contact with livestock, particularly pigs and veal calves. For instance, significantly higher rates of MRSA nasal carriage by humans in contact with pigs (farm workers, abattoir workers, veterinarians) have been noted in several epidemiological studies, with the isolates typically belonging to CC398 [12-16]. Further studies have shown an association between clinical disease resulting from LA-MRSA CC398 infection and contact with pigs or pig farms [16-20]. The impact of this can be significant locally, and this lineage can be imported into healthcare settings. For example, in a German hospital in an area with a large number of pigs, 22% of patients colonised with MRSA at admission carried ST398 [21]. Nosocomial transmission has also been reported [22]. LA-MRSA CC398, like other MRSA, may be responsible for life-threatening infections during long or frequent hospitalisations, or following wound or surgery site infections, and also increases healthcare costs resulting from screening, isolation of carriers, and decolonisation. Although pasteurisation of milk should ensure that CC398 MRSA will not enter the food chain, our finding of LA-MRSA CC398 in dairy cattle has clear public health implications for the UK. Workers on dairy farms, or individuals with regular contact with dairy cows, are likely to have a higher risk of colonisation or infection with LA-MRSA CC398 compared to the general population in the UK. LA-MRSA CC398 isolates from three of the farms where isolated were found carried SCCmec type IVa. The isolates from the other two farms carried SCCmec type V(5C2&5) c. Both of these SCCmec types have previously been found in LA-MRSA CC398 isolates [23].




Heterogeneity is seen in S. aureus CC398, with human and livestock-associated lineages being differentiated by the presence or absence of specific resistance and virulence-related genes [23-24]. In all of our isolates the absence of the scn gene, encoding the humanspecific staphylococcal complement inhibitor, and the presence of tet(M) suggested that they were all livestock-associated, as opposed to S. aureus CC398 strains which circulate in the human population independent of a livestock reservoir [23-24]. Likewise, all seven isolates lacked the lukS-PV and lukF-PV genes encoding Panton-Valentine leukocidin which is absent in LA-MRSA CC398, but is present in some, but not all, human-associated CC398 isolates [23]. Three consecutive samples from the same farm over a seven-month period were positive for LA-MRSA CC398 isolates with identical spa (t011) and SCCmec types (IVa), suggesting that this strain is able to persist in dairy herds over prolonged periods. While there are relatively few reports of LA-MRSA CC398 from dairy cattle compared to pig farms, it has been found to cause bovine mastitis [25-27]. Our findings therefore have significance to veterinary medicine, in addition to public health. The relative absence of CC398 MRSA from the UK prior to this study, when it is widespread in the rest of Europe suggests that the geographical separation of the UK from continental Europe may have delayed the spread of this lineage to the UK rather than there being any fundamental difference in husbandry or biosecurity in the UK. The authors are aware of unpublished surveys looking for potential LA-MRSA in UK dairy and pig herds that have been negative before now. These CC398-positive samples were not part of a formal prevalence study, and it is therefore unclear how common LA-MRSA CC398 isolates are in UK dairy farms or if they are present in other livestock. However, the five farms with positive samples were identified from a sample of ca. 1,500 farms, indicating a low prevalence currently.




Conclusions



This is the first description of LA-MRSA CC398 in foodproducing animals in the UK. The ability of this lineage to colonise a wide range of host species, coupled with its zoonotic potential, make this finding of significance to both veterinary and human health. Future surveillance for this LA-MRSA CC398 strain in all food-producing animal species in the UK and the evaluation of occupational risk factors for MRSA carriage and infection should be considered.





SNIP.




Table Molecular and phenotypic characteristics of meticillin-resistant Staphylococcus aureus CC398 from bulk tank milk in the United Kingdom, January to July 2012 (n=7)




SNIP...




Acknowledgments



SNIP...









New MRSA superbug strain found in UK milk




84 21 712B/y Jeremy Laurance Wednesday, 26 December 2012



A new strain of MRSA has been found in British milk, indicating that the superbug is spreading through the livestock population and poses a growing threat to human health.



The new strain, MRSA ST398, has been identified in seven samples of bulk milk from five different farms in England.



The discovery, from tests on 1,500 samples, indicates that antibiotic-resistant organisms are gaining an increasing hold in the dairy industry.




The disclosure comes amid growing concern over the use of modern antibiotics on British farms, driven by price pressure imposed by the big supermarket chains. Intensive farming with thousands of animals raised in cramped conditions means infections spread faster and the need for antibiotics is consequently greater.



Three classes of antibiotics rated as “critically important to human medicine” by the World Health Organisation – cephalosporins, fluoroquinolones and macrolides – have increased in use in the animal population by eightfold in the last decade.



The more antibiotics are used, the greater the likelihood that antibiotic-resistant bacteria, such as MRSA, will evolve.



Experts say there is no risk of MRSA infection to consumers of milk or dairy products so long as the milk is pasteurised. The risk comes from farmworkers, vets and abattoir workers, who may become infected through contact with livestock and transmit the bug to others.



The discovery was made by scientists from Cambridge University who first identified MRSA in milk in 2011. They say the latest finding of a different strain is worrying.



Mark Holmes, of the department of veterinary medicine, who led the study, published in Eurosurveillance, said: “This is definitely a worsening situation. In 2011 when we first found MRSA in farm animals, the Department of Environment, Food and Rural Affairs [Defra] initially didn’t believe it. They said we don’t have MRSA in the dairy industry in this country.”



“Now we definitely have MRSA in livestock. What is curious is that it has turned up in dairy cows when in other countries on the Continent it is principally in pigs. Could it be in pigs or poultry in this country? We don’t know.”



The MRSA superbug can cause serious infections in humans which are difficult to treat, require stronger antibiotics, and take longer to resolve. Human cases of infection with the new strain have been found in Scotland and northern England according to Defra, but no details are available.



Dr Holmes said supermarket pressure on farmers to hold down prices was leading to the overuse of antibiotics to prevent cattle getting mastitis, an infection of the udder, that might interrupt the milk supply.



“If farmers were not screwed into the ground by the supermarkets and allowed to get a fair price for their milk they would be able to use fewer antibiotics,” he said.



“Common sense tells us that anything we can do to reduce use of antibiotics will reduce the growth of resistant bugs. We want to wean our farmers off antibiotics and the only way we can do that is with better regulation.”



Vets in Norway and Denmark had much more limited prescribing powers than in the UK, he added.









MRSA found in our milk: Superbug strain can cause serious infections in humans and is resistant to antibiotics



Scientists tested 1,500 samples of bulk milk and found seven cases of MRSA ST398 from five farms in England, Scotland and Wales




The superbug can cause serious and occasionally deadly infections in humans



By Sean Poulter PUBLISHED:19:52 EST, 20 December 2012| UPDATED: 02:46 EST, 21 December 2012 Comments (47) Share



. . A potentially deadly MRSA superbug has been found in British milk for the first time.



The superbug – already a problem in farm animals on the Continent – can cause serious and occasionally deadly infections in humans and is becoming a cause of udder infections in dairy cows.



The strain of MRSA known as ST398 is resistant to antibiotics, so doctors find it difficult to treat infected people effectively.



Superbug: A strain of MRSA has been found in British milk for the first time In theory the bug should be killed off when milk is heat-treated in the pasteurisation process before it reaches the high street or doorstep. However, some people prefer unpasteurised milk and cheese in the belief it is better for them or tastes nicer.



More... Exterminate! Doctor Who-villain lookalike robot taking on superbugs could save NHS £200 million per year Scientists halt deadly MRSA outbreak by cracking genetic code and tracking down carrier in breakthrough that could save hundreds of lives each year



And farmers, vets and abattoir workers who come into contact with the cows and their calves can become infected, allowing the bug to spread into the wider community. That has happened in the Netherlands where the same strain of MRSA has caused illness among nursing home residents.



MRSA ST398 was first seen in pigs in Holland in 2003. It has since become epidemic in European and North American pig populations and has spread to poultry and cattle.



It is one of a number of superbugs that have emerged in recent years, apparently as a result of the overuse of antibiotics by farmers treating sick animals. Over time the farm animal bugs develop a resistance.



Strain: Farmers, vets and abbatoir workers who come into contact with cows and their calves can become infected The Soil Association, which campaigns for organic farming, is calling for a government investigation to establish the spread of the MRSA and a crackdown on the use of antibiotics on UK farms.



Scientists from the department of veterinary medicine at the University of Cambridge tested 1,500 samples of bulk milk and found seven cases of MRSA ST398 from five farms in England, Scotland and Wales.



They said the high level of antibiotic resistance in the bug means the findings are ‘of significance to both veterinary and human health’. Dr Mark Holmes, a senior lecturer in preventive veterinary medicine, said the discovery was made while looking for a different strain of MRSA found in cows and people.



He said: ‘Until this discovery it was always assumed that this form of livestock MRSA was a problem on the Continent, but it has now jumped the Channel. It now seems that it is established in this country – perhaps one in every 200 farms.



‘If it ends up becoming more commonplace it will, sooner or later, cause disease in people here.’



Dr Holmes said the major question is why MRSA is appearing in farm animals and whether this is linked to intensive farming and the associated heavy use of antibiotics.



He asked: ‘Should we be thinking again about the type and range of antibiotics we use in farm animals? Is it wise to have a lot of preventive use of antibiotics, particularly in dairy cows?



‘They get a lot of mastitis – udder infection – because they are driven hard to produce a lot of milk, which is the only way farmers can make money.



‘I think you have to look at the pressures the supermarkets create by screwing the farmers down so tightly on costs.’










Letter





Lethal Necrotizing Pneumonia Caused by an ST398 Staphylococcus aureus Strain














Letter



Ventilator-associated Pneumonia and MRSA ST398, Italy












Letter



Livestock-associated Methicillin-Susceptible Staphylococcus aureus ST398 Infection in Woman, Colombia












Letter




Suspected Horse-to-Human Transmission of MRSA ST398












Letter



Lethal Necrotizing Pneumonia Caused by an ST398 Staphylococcus aureus Strain











Dispatch


Methicillin-Resistant Staphylococcus aureus ST398 in Swine Farm Personnel, Belgium










Dispatch



Staphylococcus aureus ST398, New York City and Dominican Republic





Abstract


Closely related Staphylococcus aureus strains of ST398, an animal-associated strain, were identified in samples collected from humans in northern Manhattan, New York, NY, USA, and in the Dominican Republic. A large population in northern Manhattan has close ties to the Dominican Republic, suggesting international transmission.










Letter



Methicillin-Resistant Staphylococcus aureus ST398, Italy












Monday, April 18, 2011


Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry









Wednesday, May 11, 2011


Methicillin-resistant Staphylococcus aureus in Retail Meat, Detroit, Michigan, USA








Thursday, June 9, 2011


New Superbug Found in Cows and People








Thursday, August 12, 2010


Escherichia coli sequence type ST131 as the major cause of serious multidrug-resistant E. coli infections in the United States


Clin Infect Dis. 2010 Aug 1;51(3):286-94.












MRSA damn near killed me in 2001 after one of my many neck surgeries, and it’s some nasty stuff. 8 weeks vancomycin straight through top of heart via PIC long line, twice daily, and the vanco almost stopped working, had to double dose midway through. ...




NOW, today we have VRSA. no telling where that will take us...





Comparative Genomics of Vancomycin-Resistant Staphylococcus aureus Strains and Their Positions within the Clade Most Commonly Associated with Methicillin-Resistant S. aureus Hospital-Acquired Infection in the United States




doi: 10.1128/​mBio.00112-12 22 May 2012 mBio vol. 3 no. 3 e00112-12




Veronica N. Kosa,b, Christopher A. Desjardinsb, Allison Griggsb, Gustavo Cerqueirab, Andries Van Tonderc, Matthew T. G. Holdenc, Paul Godfreyb, Kelli L. Palmera, Kip Bodid, Emmanuel F. Mongodine, Jennifer Wortmanb, Michael Feldgardenb, Trevor Lawleyc, Steven R. Gillf, Brian J. Haasb, Bruce Birrenb, and Michael S. Gilmorea,b





Address correspondence to Michael S. Gilmore, michael_gilmore@meei.harvard.edu.



Editor Paul Keim, Northern Arizona University



ABSTRACT



Methicillin-resistant Staphylococcus aureus (MRSA) strains are leading causes of hospital-acquired infections in the United States, and clonal cluster 5 (CC5) is the predominant lineage responsible for these infections. Since 2002, there have been 12 cases of vancomycin-resistant S. aureus (VRSA) infection in the United States—all CC5 strains. To understand this genetic background and what distinguishes it from other lineages, we generated and analyzed high-quality draft genome sequences for all available VRSA strains. Sequence comparisons show unambiguously that each strain independently acquired Tn1546 and that all VRSA strains last shared a common ancestor over 50 years ago, well before the occurrence of vancomycin resistance in this species. In contrast to existing hypotheses on what predisposes this lineage to acquire Tn1546, the barrier posed by restriction systems appears to be intact in most VRSA strains. However, VRSA (and other CC5) strains were found to possess a constellation of traits that appears to be optimized for proliferation in precisely the types of polymicrobic infection where transfer could occur. They lack a bacteriocin operon that would be predicted to limit the occurrence of non-CC5 strains in mixed infection and harbor a cluster of unique superantigens and lipoproteins to confound host immunity. A frameshift in dprA, which in other microbes influences uptake of foreign DNA, may also make this lineage conducive to foreign DNA acquisition.



IMPORTANCE



Invasive methicillin-resistant Staphylococcus aureus (MRSA) infection now ranks among the leading causes of death in the United States. Vancomycin is a key last-line bactericidal drug for treating these infections. However, since 2002, vancomycin resistance has entered this species. Of the now 12 cases of vancomycin-resistant S. aureus (VRSA), each was believed to represent a new acquisition of the vancomycin-resistant transposon Tn1546 from enterococcal donors. All acquisitions of Tn1546 so far have occurred in MRSA strains of the clonal cluster 5 genetic background, the most common hospital lineage causing hospital-acquired MRSA infection. To understand the nature of these strains, we determined and examined the nucleotide sequences of the genomes of all available VRSA. Genome comparison identified candidate features that position strains of this lineage well for acquiring resistance to antibiotics in mixed infection.



Footnotes



Citation Kos VN, et al. 2012. Comparative genomics of vancomycin-resistant Staphylococcus aureus strains and their positions within the clade most commonly associated with methicillin-resistant S. aureus hospital-acquired infection in the United States. mBio 3(3):e00112-12. doi:10.1128/mBio.00112-12.



Received 13 April 2012 Accepted 24 April 2012 Published 22 May 2012 Copyright © 2012 Kos et al.



This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.





 
 
 
 
 
TSS

Sunday, April 8, 2012

US FDA told to stop certain antibiotics being used as growth promoters

Subject: US FDA told to stop certain antibiotics being used as growth promoters

Veterinary Record2012;170:348 doi:10.1136/vr.e2472

News & Reports

Antibiotic Resistance

US FDA told to stop certain antibiotics being used as growth promoters

A FEDERAL court in the USA has ruled that the US Food and Drug Administration (FDA) should start proceedings to withdraw the approval of certain uses of antibiotics used in food production.

The ruling, by United States Magistrate Judge Theodore H. Katz on March 22, relates to what the FDA currently refers to as ‘production uses’ of penicillins and tetracyclines in food-producing …





http://veterinaryrecord.bmj.com/content/170/14/348.2.extract?etoc






Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock



Lance B. Pricea, Marc Steggerb, Henrik Hasmanc, Maliha Aziza, Jesper Larsenb, Paal Skytt Andersenb, Talima Pearsond, Andrew E. Watersa, Jeffrey T. Fosterd, James Schuppa, John Gillecea, Elizabeth Driebea, Cindy M. Liua,d, Burkhard Springere, Irena Zdovcf, Antonio Battistig, Alessia Francog, Jacek Żmudzkih, Stefan Schwarzi, Patrick Butayej,k, Eric Jouyl, Constanca Pombam, M. Concepción Porreron, Raymond Ruimyo, Tara C. Smithp, D. Ashley Robinsonq, J. Scott Weeser, Carmen Sofia Arriolas, Fangyou Yut, Frederic Laurentu, Paul Keima,d, Robert Skovb, and Frank M. Aarestrupc

+ Author Affiliations

snip...


Address correspondence to Lance B. Price, lprice@tgen.org.

Editor Fernando Baquero, Ramón y Cajal University Hospital



ABSTRACT

Since its discovery in the early 2000s, methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398) has become a rapidly emerging cause of human infections, most often associated with livestock exposure. We applied whole-genome sequence typing to characterize a diverse collection of CC398 isolates (n = 89), including MRSA and methicillin-susceptible S. aureus (MSSA) from animals and humans spanning 19 countries and four continents. We identified 4,238 single nucleotide polymorphisms (SNPs) among the 89 core genomes. Minimal homoplasy (consistency index = 0.9591) was detected among parsimony-informative SNPs, allowing for the generation of a highly accurate phylogenetic reconstruction of the CC398 clonal lineage. Phylogenetic analyses revealed that MSSA from humans formed the most ancestral clades. The most derived lineages were composed predominantly of livestock-associated MRSA possessing three different staphylococcal cassette chromosome mec element (SCCmec) types (IV, V, and VII-like) including nine subtypes. The human-associated isolates from the basal clades carried phages encoding human innate immune modulators that were largely missing among the livestock-associated isolates. Our results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA. The lineage appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance. Further analyses are required to estimate the number of independent genetic events leading to the methicillin-resistant sublineages, but the diversity of SCCmec subtypes is suggestive of strong and diverse antimicrobial selection associated with food animal production.



IMPORTANCE

Modern food animal production is characterized by densely concentrated animals and routine antibiotic use, which may facilitate the emergence of novel antibiotic-resistant zoonotic pathogens. Our findings strongly support the idea that livestock-associated MRSA CC398 originated as MSSA in humans. The jump of CC398 from humans to livestock was accompanied by the loss of phage-carried human virulence genes, which likely attenuated its zoonotic potential, but it was also accompanied by the acquisition of tetracycline and methicillin resistance. Our findings exemplify a bidirectional zoonotic exchange and underscore the potential public health risks of widespread antibiotic use in food animal production.



Footnotes

Citation Price LB, et al. 2012. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. mBio 3(1):e00305-11. doi:10.1128/mBio.00305-11.

Received 19 December 2011 Accepted 3 January 2012 Published 21 February 2012 Copyright © 2012 Price et al.



This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.



http://mbio.asm.org/content/3/1/e00305-11.abstract?etoc





http://mbio.asm.org/content/3/1/e00305-11.full.pdf+html







Thursday, March 1, 2012


Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock



http://staphmrsa.blogspot.com/2012/03/staphylococcus-aureus-cc398-host.html







SEE ALSO ;



Tuesday, January 17, 2012

In-feed antibiotic effects on the swine intestinal microbiome

http://staphmrsa.blogspot.com/2012/01/in-feed-antibiotic-effects-on-swine.html





Thursday, February 9, 2012

Occurrence and distribution of Staphylococcus aureuslineages among zoo animals

http://staphmrsa.blogspot.com/2012/02/occurrence-and-distribution-of.html






Thursday, June 9, 2011

New Superbug Found in Cows and People

http://staphmrsa.blogspot.com/2011/06/new-superbug-found-in-cows-and-people.html





Wednesday, May 11, 2011

Methicillin-resistant Staphylococcus aureus in Retail Meat, Detroit, Michigan, USA

http://staphmrsa.blogspot.com/2011/05/methicillin-resistant-staphylococcus.html





Monday, April 18, 2011

Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry

http://staphmrsa.blogspot.com/2011/04/multidrug-resistant-staphylococcus.html





http://staphmrsa.blogspot.com/




TSS

Thursday, March 1, 2012

Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock

Staphylococcus aureus CC398: Host Adaptation and Emergence of Methicillin Resistance in Livestock



Lance B. Pricea, Marc Steggerb, Henrik Hasmanc, Maliha Aziza, Jesper Larsenb, Paal Skytt Andersenb, Talima Pearsond, Andrew E. Watersa, Jeffrey T. Fosterd, James Schuppa, John Gillecea, Elizabeth Driebea, Cindy M. Liua,d, Burkhard Springere, Irena Zdovcf, Antonio Battistig, Alessia Francog, Jacek Żmudzkih, Stefan Schwarzi, Patrick Butayej,k, Eric Jouyl, Constanca Pombam, M. Concepción Porreron, Raymond Ruimyo, Tara C. Smithp, D. Ashley Robinsonq, J. Scott Weeser, Carmen Sofia Arriolas, Fangyou Yut, Frederic Laurentu, Paul Keima,d, Robert Skovb, and Frank M. Aarestrupc

+ Author Affiliations

snip...


Address correspondence to Lance B. Price, lprice@tgen.org.

Editor Fernando Baquero, Ramón y Cajal University Hospital



ABSTRACT

Since its discovery in the early 2000s, methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 (CC398) has become a rapidly emerging cause of human infections, most often associated with livestock exposure. We applied whole-genome sequence typing to characterize a diverse collection of CC398 isolates (n = 89), including MRSA and methicillin-susceptible S. aureus (MSSA) from animals and humans spanning 19 countries and four continents. We identified 4,238 single nucleotide polymorphisms (SNPs) among the 89 core genomes. Minimal homoplasy (consistency index = 0.9591) was detected among parsimony-informative SNPs, allowing for the generation of a highly accurate phylogenetic reconstruction of the CC398 clonal lineage. Phylogenetic analyses revealed that MSSA from humans formed the most ancestral clades. The most derived lineages were composed predominantly of livestock-associated MRSA possessing three different staphylococcal cassette chromosome mec element (SCCmec) types (IV, V, and VII-like) including nine subtypes. The human-associated isolates from the basal clades carried phages encoding human innate immune modulators that were largely missing among the livestock-associated isolates. Our results strongly suggest that livestock-associated MRSA CC398 originated in humans as MSSA. The lineage appears to have undergone a rapid radiation in conjunction with the jump from humans to livestock, where it subsequently acquired tetracycline and methicillin resistance. Further analyses are required to estimate the number of independent genetic events leading to the methicillin-resistant sublineages, but the diversity of SCCmec subtypes is suggestive of strong and diverse antimicrobial selection associated with food animal production.



IMPORTANCE

Modern food animal production is characterized by densely concentrated animals and routine antibiotic use, which may facilitate the emergence of novel antibiotic-resistant zoonotic pathogens. Our findings strongly support the idea that livestock-associated MRSA CC398 originated as MSSA in humans. The jump of CC398 from humans to livestock was accompanied by the loss of phage-carried human virulence genes, which likely attenuated its zoonotic potential, but it was also accompanied by the acquisition of tetracycline and methicillin resistance. Our findings exemplify a bidirectional zoonotic exchange and underscore the potential public health risks of widespread antibiotic use in food animal production.



Footnotes

Citation Price LB, et al. 2012. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. mBio 3(1):e00305-11. doi:10.1128/mBio.00305-11.

Received 19 December 2011 Accepted 3 January 2012 Published 21 February 2012 Copyright © 2012 Price et al.



This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.



http://mbio.asm.org/content/3/1/e00305-11.abstract?etoc




http://mbio.asm.org/content/3/1/e00305-11.full.pdf+html





SEE ALSO ;



Tuesday, January 17, 2012



In-feed antibiotic effects on the swine intestinal microbiome


http://staphmrsa.blogspot.com/2012/01/in-feed-antibiotic-effects-on-swine.html





Thursday, February 9, 2012



Occurrence and distribution of Staphylococcus aureuslineages among zoo animals



http://staphmrsa.blogspot.com/2012/02/occurrence-and-distribution-of.html





Thursday, June 9, 2011



New Superbug Found in Cows and People



http://staphmrsa.blogspot.com/2011/06/new-superbug-found-in-cows-and-people.html





Wednesday, May 11, 2011



Methicillin-resistant Staphylococcus aureus in Retail Meat, Detroit, Michigan, USA


http://staphmrsa.blogspot.com/2011/05/methicillin-resistant-staphylococcus.html




Monday, April 18, 2011



Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry


http://staphmrsa.blogspot.com/2011/04/multidrug-resistant-staphylococcus.html




http://staphmrsa.blogspot.com/





TSS

Thursday, February 9, 2012

Occurrence and distribution of Staphylococcus aureuslineages among zoo animals





Original Research Article



In Press, Accepted Manuscript, Available online 2 February 2012



Carmen Espinosa-Gongora, Dorota Chrobak, Arshnee Moodley, Mads Frost Bertelsen, Luca Guardabassi





Abstract

The current knowledge of the occurrence and diversity of Staphylococcus aureus in animals is largely biased in favour MRSA and domestic animals. In order to generate novel information on the ecology and population structure of this bacterial species in the animal kingdom, we investigated the occurrence and genotypic diversity of S. aureus in a range of animal species kept at the Copenhagen Zoo. We sampled 146 animals belonging to 25 mammalian species and 21 reptiles belonging to six species. A total of 59 S. aureus isolates were found in 10 of the 25 mammalian species tested. All isolates were MSSA belonging to fourteen spa types, including three novel spa types. MLST revealed the occurrence of seven STs. The study of the ecology of commensal S. aureus in captive wild animals revealed that ST133 has a broader host range than previously thought.









Thursday, June 9, 2011


New Superbug Found in Cows and People






Wednesday, May 11, 2011


Methicillin-resistant Staphylococcus aureus in Retail Meat, Detroit, Michigan, USA






Monday, April 18, 2011


Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry





 

TSS

Tuesday, January 17, 2012

In-feed antibiotic effects on the swine intestinal microbiome

In-feed antibiotic effects on the swine intestinal microbiome


Torey Loofta,1, Timothy A. Johnsonb,c,1, Heather K. Allena,1, Darrell O. Baylesa, David P. Alta, Robert D. Stedtfeldb,d, Woo Jun Sulb,c, Tiffany M. Stedtfeldb, Benli Chaib, James R. Coleb, Syed A. Hashshamb,d, James M. Tiedjeb,c,2, and Thad B. Stantona,2 aAgricultural Research Service, National Animal Disease Center, US Department of Agriculture, Ames, IA 50010; and bCenter for Microbial Ecology, cDepartment of Crop and Soil Science, and dDepartment of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823


Contributed by James M. Tiedje, December 19, 2011 (sent for review July 12, 2011)


Antibiotics have been administered to agricultural animals for disease treatment, disease prevention, and growth promotion for over 50 y. The impact of such antibiotic use on the treatment of human diseases is hotly debated. We raised pigs in a highly controlled environment, with one portion of the littermates receiving a diet containing performance-enhancing antibiotics [chlortetracycline, sulfamethazine, and penicillin (known as ASP250)] and the other portion receiving the same diet but without the antibiotics. We used phylogenetic, metagenomic, and quantitative PCR-based approaches to address the impact of antibiotics on the swine gut microbiota. Bacterial phylotypes shifted after 14 d of antibiotic treatment, with the medicated pigs showing an increase in Proteobacteria (1–11%) compared with nonmedicated pigs at the same time point. This shift was driven by an increase in Escherichia coli populations. Analysis of the metagenomes showed that microbial functional genes relating to energy production and conversion were increased in the antibiotic-fed pigs. The results also indicate that antibiotic resistance genes increased in abundance and diversity in the medicated swine microbiome despite a high background of resistance genes in nonmedicated swine. Some enriched genes, such as aminoglycoside O-phosphotransferases, confer resistance to antibiotics that were not administered in this study, demonstrating the potential for indirect selection of resistance to classes of antibiotics not fed. The collateral effects of feeding subtherapeutic doses of antibiotics to agricultural animals are apparent and must be considered in cost-benefit analyses.


intestinal microbiota | microbiome shifts | swine bacteria | BioTrove microarray | metagenomics


snip...


Conclusions


The results show that even a low, short-term dose of in-feed antibiotics increases the abundance and diversity of antibiotic resistance genes, including resistance to antibiotics not administered, and increases the abundance of E. coli, a potential human pathogen. Additionally, analysis of the metagenomes implicated functions potentially involved with improved feed efficiency. The study design featured environmental control in a single uniform inoculum source (the mother), control of the host genetics, no exposure of the sow or piglets to antibiotics except for the treatment, and identical diet except for the inclusion of ASP250 in one group. Future studies should include other in-feed antibiotics, multiple litters of swine with robust replication, and the identification of the antibiotic-induced mechanisms that lead to increased feed efficiency. Implications of antibiotic resistance on human and animal health need to be taken into account when discussing agricultural management policies and evaluating alternatives to traditional antibiotics. With the use of antibiotics in animal agriculture at a crossroads, studies like this and others that highlight the collateral effects of antibiotic use are needed.






Study provides new insights into antibiotics and pig feeds Contact: Layne Cameron, University Relations, Office: (517) 353-8819, Cell: (765) 748-4827, layne.cameron@ur.msu.edu; Thad Stanton, USDA-ARS National Animal Disease Center, Office: (515) 337-7244, thad.stanton@ars.usda.gov; James Tiedje, Crop and Soil Sciences, Office: (517) 355-0271, ext. 1287, tiedjej@msu.edu


Published: Jan. 16, 2012 E-mail Editor ShareThis


Jim Tiedje, University Distinguished professor of microbiology and molecular genetics, is the co-author of a comprehensive study on antibiotics use in pig feed. Photo by Kurt Stepnitz.


Antibiotics in pig feed are increasing antibiotic resistance genes in gastronintestinal microbes in pigs. Photo courtesy of MSU.


Click on an image to view a larger or high-resolution version.


Related Links PNAS paper (opens in new window) EAST LANSING, Mich. — Antibiotics in pig feed increased the number of antibiotic resistant genes in gastrointestinal microbes in pigs, according to a study conducted by Michigan State University and the U.S. Department of Agriculture’s Agricultural Research Service.


Published in the current edition of the Proceedings of the National Academy of Sciences, the comprehensive study focused on understanding the effects of conventional, in-feed antibiotics in U.S. farms.


For decades, many producers of pigs, chickens and other farm animals have used antibiotics not only to protect their livestock from disease, but also to boost growth rates and enhance feed efficiency, a measure of how well animals convert feed into weight gains.


Scientists don’t know precisely how antibiotics enhance growth rates and feed efficiency, but they are concerned that on-farm use of these medications may contribute to the development of strains of microbes resistant to conventional antibiotics, which are potentially harmful to humans and animals, said James Tiedje, MSU University Distinguished Professor of microbiology and molecular genetics and of crop and soil sciences.


“The growth of antibiotic resistance in pathogens is a huge challenge for society around the world,” said Tiedje, an MSU AgBioResearch scientist. “Studies to understand what contributes to the spread and what interventions can help control the problem are vital.”


Additional findings include:


Both diversity and abundance of antibiotic resistance genes increased in the intestinal microbial communities of the pigs treated with antibiotics. Longer term studies are needed. Some of the genes found in the treated pigs were unexpected and usually linked to antibiotics not used in the study. Microbial genes associated with production and use of energy by microbes increased in abundance in the antibiotic-fed pigs, which may shed light on how antibiotics increase livestock growth and feed efficiency. E. coli populations increased in the intestines of the treated pigs. Further study is needed to clarify this observation. “To our knowledge, this study is the first of its kind to look at the collateral impacts of in-feed antibiotic use in farm animals, using a comprehensive approach to detect shifts in the function and the makeup or membership of the microbial community in the model animal’s gastrointestinal tract,” said Torey Looft, USDA researcher.


Additional MSU researchers included Tim Johnson, doctoral student; Robert Stedtfeld, civil and environmental engineering research associate; Woo Jun Sul, doctoral student; Tiffany Stedtfeld, civil and environmental engineering technical aide; Benli Chai, information technologist, Center for Microbial Ecology; James Cole, assistant professor at the Center for Microbial Ecology; and Syed Hashsham, civil and environmental engineering professor.


Funding was provided by MSU’s Environmental Science and Policy Program initiative on Pharmaceuticals in the Environment, ARS and the National Institutes of Health and through the Alliance for the Prudent Use of Antibiotics program on Reservoirs of Antibiotic Resistance.


###


Michigan State University has been working to advance the common good in uncommon ways for more than 150 years. One of the top research universities in the world, MSU focuses its vast resources on creating solutions to some of the world’s most pressing challenges, while providing life-changing opportunities to a diverse and inclusive academic community through more than 200 programs of study in 17 degree-granting colleges.


As the USDA’s chief scientific research agency, ARS is leading America toward a better future through agricultural research and information. ARS conducts research to develop and transfer solutions to help answer agricultural questions that impact Americans every day.











Thursday, June 9, 2011



New Superbug Found in Cows and People









Wednesday, May 11, 2011



Methicillin-resistant Staphylococcus aureus in Retail Meat, Detroit, Michigan, USA









Monday, April 18, 2011



Multidrug-Resistant Staphylococcus aureus in US Meat and Poultry











TSS

Thursday, June 9, 2011

New Superbug Found in Cows and People

New Superbug Found in Cows and People


by Jocelyn Kaiser on 2 June 2011, 6:30 PM|



A novel form of deadly drug-resistant bacteria that hides from a standard test has turned up in Europe. Researchers found the so-called MRSA strain in both dairy cows and humans in the United Kingdom, suggesting that it might be passed from dairies to the general population. But before you toss your milk, don't panic: The superbug isn't a concern in pasteurized dairy products.

MRSA, short for methicillin-resistant Staphylococcus aureus, is a drug-resistant form of the widespread and normally harmless S. aureus bacteria. Many people walk around with MRSA in their noses or on their skin yet don't get sick. But in some hospital patients and people with weakened immune systems, MRSA thrives, and it is blamed for about 19,000 hospital deaths a year in the United States.

Mark Holmes of the University of Cambridge in the United Kingdom and colleagues stumbled upon the new strain while studying mastitis, or infected udders, in U.K. dairy cows. Some milk samples from sick cows contained S. aureus bacteria that grew in the presence of antibiotics, which is one test for MRSAs. Yet the same samples turned up negative for the drug-defying bacterium when the team used PCR, a DNA amplification technique, to detect a gene called mecA, which is found in all MRSA strains.

The PCR test doesn't always pick up variants of the gene it's meant to detect, however. To check this, the researchers sent a cow S. aureus sample to the Wellcome Trust Sanger Institute in Cambridge, which sequenced the bacterium's entire genome. "Lo and behold, there was a mecA gene there," one whose sequence overlapped with the better-known mecA by a surprisingly low 60%, Holmes said today in a press conference.

The researchers then looked for this mecA gene in people. They tested 74 samples of S. aureus isolated from people from the United Kingdom and Denmark that were drug resistant in the antibiotic growth test but not in the PCR test—most from carriers but some from patients who were sickened by MRSA. They found the new mecA in about two-thirds of the samples, they report today in The Lancet Infectious Diseases. A nearly identical mecA gene has also now been reported in human samples from Germany and Ireland.

The strain is still relatively rare—it probably makes up less than 1% of all detected MRSA cases, the U.K. team says. But its prevalence appears to have risen in the past decade. "More likely it's been around in the environment for a long time, and it's just getting into the human population," says University College Dublin microbiologist David Coleman, whose team reports on the Irish samples today in Antimicrobial Agents and Chemotherapy.

The new superbug probably isn't leading to missed infections, at least in the United Kingdom, because hospitals that suspect a patient is infected with an MRSA nearly always use the antibiotic growth test in addition to PCR, Holmes says. (Patients with a confirmed infection then receive antibiotics that work on MRSAs.) However, many hospitals in continental Europe are moving toward using only PCR tests; this is a warning that those tests need to be modified to test for the new mecA gene, Holmes says.

The study also points to dairy cows as a possible reservoir for the bug, just as pigs seem to pass MRSA to humans in the Netherlands. The bug probably doesn't get to humans through the milk supply, because almost all milk in the United Kingdom and Denmark is pasteurized, a process that kills bacteria. But workers who come into contact with infected dairy cows could be carriers. Holmes's team reports "circumstantial evidence" for this, such as the fact that genetic subtypes of the human and cow samples from the same geographical areas were nearly identical. "The main worry would be that these cows represent a pool of the bacteria" that farm workers spread into the human population, Holmes says.

The big mystery, says Patrick Schlievert of the University of Minnesota, Twin Cities, is where the unusual mecA gene came from. One possibility is that it originated long ago in a patient treated with multiple antibiotics and later somehow got into cows. "This should trigger an awful lot of research to figure out what is going on here," he says.



http://news.sciencemag.org/sciencenow/2011/06/new-superbug-found-in-cows-and-p.html?ref=hp




The Lancet Infectious Diseases, Early Online Publication, 3 June 2011


doi:10.1016/S1473-3099(11)70126-8Cite or Link Using DOI



Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study


Laura García-Álvarez PhD a, Matthew TG Holden PhD b, Heather Lindsay BSc a, Cerian R Webb PhD a, Derek FJ Brown PhD c, Martin D Curran PhD c, Enid Walpole FIMLS c, Karen Brooks BSc b, Derek J Pickard PhD b, Christopher Teale MRCVS d, Prof Julian Parkhill PhD b, Stephen D Bentley PhD b, Giles F Edwards FRCPath e, E Kirsty Girvan MSc e, Angela M Kearns PhD f, Bruno Pichon PhD f, Robert LR Hill PhD f, Anders Rhod Larsen PhD g, Robert L Skov MD g, Prof Sharon J Peacock PhD h, Prof Duncan J Maskell PhD a, Dr Mark A Holmes VetMB a


Summary

Background

Animals can act as a reservoir and source for the emergence of novel meticillin-resistant Staphylococcus aureus (MRSA) clones in human beings. Here, we report the discovery of a strain of S aureus (LGA251) isolated from bulk milk that was phenotypically resistant to meticillin but tested negative for the mecA gene and a preliminary investigation of the extent to which such strains are present in bovine and human populations.

Methods

Isolates of bovine MRSA were obtained from the Veterinary Laboratories Agency in the UK, and isolates of human MRSA were obtained from diagnostic or reference laboratories (two in the UK and one in Denmark). From these collections, we searched for mecA PCR-negative bovine and human S aureus isolates showing phenotypic meticillin resistance. We used whole-genome sequencing to establish the genetic basis for the observed antibiotic resistance.

Findings

A divergent mecA homologue (mecALGA251) was discovered in the LGA251 genome located in a novel staphylococcal cassette chromosome mec element, designated type-XI SCCmec. The mecALGA251 was 70% identical to S aureus mecA homologues and was initially detected in 15 S aureus isolates from dairy cattle in England. These isolates were from three different multilocus sequence type lineages (CC130, CC705, and ST425); spa type t843 (associated with CC130) was identified in 60% of bovine isolates. When human mecA-negative MRSA isolates were tested, the mecALGA251 homologue was identified in 12 of 16 isolates from Scotland, 15 of 26 from England, and 24 of 32 from Denmark. As in cows, t843 was the most common spa type detected in human beings.

Interpretation

Although routine culture and antimicrobial susceptibility testing will identify S aureus isolates with this novel mecA homologue as meticillin resistant, present confirmatory methods will not identify them as MRSA. New diagnostic guidelines for the detection of MRSA should consider the inclusion of tests for mecALGA251.

Funding

Department for Environment, Food and Rural Affairs, Higher Education Funding Council for England, Isaac Newton Trust (University of Cambridge), and the Wellcome Trust.

a Department of Veterinary Medicine, University of Cambridge, UK

b The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK

c Health Protection Agency, Addenbrooke's Hospital, Cambridge, UK

d Veterinary Laboratories Agency, Shrewsbury, UK

e Scottish MRSA Reference Laboratory, NHS Greater Glasgow and Clyde, Stobhill Hospital, Glasgow, UK

f Microbiology Services Division, Health Protection Agency, London, UK

g Department of Antimicrobial Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark

h Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK

Correspondence to: Dr Mark A Holmes, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK



http://www.thelancet.com/journals/laninf/article/PIIS1473-3099(11)70126-8/abstract





http://staphmrsa.blogspot.com/





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