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The unit of General Bacteriology deals with pathogenic bacteria of animals (among others National Reference Laboratory for mycoplasma infections and for typhoid Salmonella) and also has a spearhead in antibiotic resistance where the molecular epidemiology of antimicrobial resistant bacteria and alternatives to the use of antibiotics are studied.

Antibiotic resistance surveillances in Salmonella serotypes and pathogenic E. coli from pigs and cattle have been conducted for years. In the beginning of this year, the surveillance activities were expanded widely with the start of two new surveillances: the resistance surveillance for commensal Escherichia coli and enterococci; and a surveillance for the occurrence of Methicillin Resistant Staphylococcus aureus (MRSA) in poultry.

Antibiotic resistance surveillance and emergence of cephalosporine resistance (ESBLs/AmpC)

The purpose of the new surveillance of commensal E. coli and enterococci in chickens, calves, cattle and pigs is to be able to evaluate interventions to reduce resistance.

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A baseline study (Abrisk) will be conducted in the coming years to determine the trends. The adjustment of trends will clarify the effect of a possible intervention. It can also point to a specific development of resistance. For other Salmonella and pathogen E. coli, a great deal of data is already available. The epidemiology of these germs is however very different from the commensals.

Zoonotic germs are actively controlled, and pathogenic germs have a specific epidemiology, where they are present only temporarily in the animal, and where treatment can be provided against them. The most important trend reported in these germs is the enormous increase of cephalosporin resistance (ESBLs/AmpC mediated resistance).

A study on this subject in E. coli of broilers was recently concluded. It showed that the situation in chickens is dramatic, with 40% of the E. coli strains being resistant, 60% of the animals positive, and 100% of the farms positive. The genes present were highly diverse and were located on different mobile genetic elements. Risk factors were also investigated, and the most important risk factor was the incubating facility. In addition, human strains from people from Africa were also studied. The transferability of one of these resistances seems to have gone smoothly and rapidly. Unfortunately, there is no directly comparable information available on the occurrence of ESBLs and AmpCs among other animal species. There are currently no specific research projects on the subject.

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We see also a rise of this resistance in Salmonella, where a number of striking outbreaks were characterised further. The salmonella report for this year shows that for all salmonella serotypes together cephalosporin resistance rose to 10% . In S. Paratyphy B, already more than 35% of the cephalosporin strains are resistant. In pathogen E. coli of pigs (see report), resistance increased tenfold between 2007 and 2010. Nearly 20% of the strains were resistant last year. We see a similar trendin pathogenic E. coli of cattle.

This rising trend is likely to continue in the coming years. This can seriously mortgage future treatments in veterinary medicine. Further research into the background of this resistance is an absolute necessity to understand the epidemiology thereof and to be able to propose interventions.


A second new surveillance is determining the occurrence and diversity of MRSA in poultry. Here, some 450 different farms will be sampled by the end of 2011. These are both egg-laying farms and poultry-meat producing farms. Previous research has shown that MRSA can occur in these animals, but the degree of that occurrence could not be assessed. This study will provide a good picture of the problem of MRSA in poultry.

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Since 2005, when a new type of MRSA in pigs was reported, it has become clear that this germ has spread in different ecosystems (voir Staphylocoque aureus résistant à la méthicilline). Various national and international surveillances (voir rapport MRSA et rapport de l'EFSA), have shown that MRSA ST398 or LA-MRSA (livestock associated MRSA) is very frequent in pigs in certain countries, but virtually nonexistent in others. Belgium is one of the three countries where MRSA occurs the most.

In addition to surveillances, there are several ongoing research projects on MRSA. In the first place, the epidemiology of this resistance is investigated (project MRSA-CO). Here, emphasis is placed on the reservoir of methicillin resistant genes (mecA). Here, all staphylococci (i.e. also non-aureus staphylococci) are investigated in animals for the presence of mecA. The initial results of this study show that there is a reservoir of resistance in these germs too. These studies moreover show that, apart from MRSA ST398, susceptible ST398 strains are still circulating, and that there is a wide reservoir of the mobile genetic element (an SCC homologous element).

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A new project has been launched (project EMIDA MRSA) that focuses on the diversity of MRSA at European level. It is clear that MRSA is widely dispersed among domesticated animals (pigs, poultry and cattle). Fortunately, the pathogenicity of this strain is not high, but since the virulence genes, which can enhance the pathogenicity of the strain, are located on mobile genetic elements, it is important to keep a close eye on the eventual spreading of these virulence genes in LA-MRSA.

Alternative to resistance to antibiotics

In other research projects we have studied the best control possibilities. (projets MRSA IWT et MRSA-phages).

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The epidemiology is studied at farm level first, and then the germ-host interactions. These on-going studies show that the germ spread very rapidly and thus has a tendency to become endemic.

As alternatives to limit the spread of the germ, the use of disinfectants is being considered, as is the use of bacteriophages, and derived phage lysins. Given the enormous contamination in positive farms (both of animals and the environment, including the farmer and his family), it will be difficult to get negative farms.

A solution is therefore not within reach and further research is urgently needed. At present, negative farms must try to remain negative, and thus livestock breeders must check, whenever new animals are introduced, whether they come from a negative farm.

CODA-CERVA Publications on the subject : "Antibiotic resistance surveillance and emergence of cephalosporine resistance"

Escherichia coli strains from Kenyan patients carrying conjugatively transferable broad-spectrum {beta}-lactamase, qnr, aac(6')-Ib-cr and 16S rRNA methyltransferase genes

Presence of extended-spectrum {beta}-lactamase-producing Escherichia coli in wild geese

In situ ESBL conjugation from avian to human Escherichia coli during cefotaxime administration

Risk factors for ceftiofur resistance in Escherichia coli from Belgian broilers

Complete nucleotide sequence of CTX-M-15-plasmids from clinical Escherichia coli isolates: insertional events of transposons and insertion sequences.

Molecular characterisation of Vibrio cholerae O1 strains carrying an SXT/R391-like element from cholera outbreaks in Kenya: 1994-2007

Broad-spectrum beta-lactamases among Enterobacteriaceae of animal origin: molecular aspects, mobility and impact on public health

Prevalence and persistence of antimicrobial resistance in broiler indicator bacteria

Comparative analysis of extended-spectrum-{beta}-lactamase-carrying plasmids from different members of Enterobacteriaceae isolated from poultry, pigs and humans: evidence for a shared {beta}-lactam resistance gene pool?

Prevalence of antimicrobial resistance among bacterial pathogens isolated from cattle in different European countries: 2002-2004

Occurrence of antimicrobial resistance among bacterial pathogens and indicator bacteria in pigs in different European countries from year 2002 - 2004: the ARBAO-II study

Diversity of extended-spectrum beta-lactamases and class C beta-lactamases among cloacal Escherichia coli Isolates in Belgian broiler farms

Dissemination of an extended-spectrum-beta-lactamase blaTEM-52 gene-carrying IncI1 plasmid in various Salmonella enterica serovars isolated from poultry and humans in Belgium and France between 2001 and 2005

Clonal emergence of extended-spectrum beta-lactamase (CTX-M-2)-producing Salmonella enterica serovar Virchow isolates with reduced susceptibilities to ciprofloxacin among poultry and humans in Belgium and France (2000 to 2003)

Genes and mutations conferring antimicrobial resistance in Salmonella: an update

The clonal spread of multidrug-resistant non-typhi Salmonella serotypes

Salmonella resistant to extended-spectrum cephalosporins: prevalence and epidemiology

Salmonella genomic island 1 multidrug resistance gene clusters in Salmonella enterica serovar Agona isolated in Belgium in 1992 to 2002

Salmonella agona harboring genomic island 1-A

CODA-CERVA publications on the subject : "MRSA"

Diversity of accessory genome of human and livestock-associated ST398 methicillin resistant Staphylococcus aureus strains

Methicillin-resistant Staphylococcus aureus (MRSA) in food production animals

Methicillin-resistant Staphylococcus aureus (MRSA) ST398 associated with clinical and subclinical mastitis in Belgian cows

Comparison of fingerprinting methods for typing methicillin-resistant Staphylococcus aureus sequence type 398

Methicillin-resistant Staphylococcus aureus ST398 in swine farm personnel, Belgium

Methicillin-resistant Staphylococcus aureus in poultry