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Table 1.1 Suggested antimicrobials, by bacteria, for inclusion for antimicrobial susceptibility testing in a programme of integrated surveillance of antimicrobial resistance in foodborne
bacteria
i ii
iii iv
v vi
vii viii
ix x
xi Recommended antimicrobials used for sur veillance of Campylobacter jejuni and Campylobacter coli.
Cefepime is used in the European Union EU to distinguish bet ween AmpC and ESBL. Lincosamides are used in the treatment of some infections caused by Campylobacter.
Resistance towards er y thromycin reflects a zithromycin resistance. Nitrofurantoin is used in the United States of America for testing Gram-positive bacteria.
It is optional for Enterococcus to be tested for nitrofurantoin. Temocillin is included as a marker to detect the bla
OX A-48
genot ype. To screen for ciprofloxacin resistance in Salmonella spp. when disk dif fusion is used.
Nalidixic acid is used in Campylobacter to identif y rare mutations. Trimethoprim-sulfamethoxa zole can be used instead of using sulfisoxa zole or trimethoprim alone.
Dox ycycline may be used instead of tetracycline. Salmonella, E. coli
Gentamicin Chloramphenicol
Imipenem Meropenem
Cefoxitin Cefatoxime
or Ceftriaxone Ceftazidime
Cefepime
ii
Tigecycline
Azithromycin Nitrofurantoin
v
Ampicillin Amoxicillin
Temocillin
vii
Colistin Ciproloxacin
Nalidixic acid Peloxacin
viii
Sulisoxazole
x
Tetracycline Trimethoprim
Campylobacter
i
Gentamicin Streptomycin
Clindamycin
iii
Erythromycin
iv
Ampicillin
Ciproloxacin Nalidixic acid
ix
Tetracycline
xi
Enterococcus Gentamicin
Streptomycin Chloramphenicol
Vancomycin Teicoplanin
Tigecycline Daptomycin
Erythromycin Nitrofurantoin
vi
Ampicillin
Ciproloxacin
Quinupristin-dalfopristin Tetracycline
Staphylococcus Gentamicin
Chloramphenicol Cefoxitin
Vancomycin
Clindamycin Erythromycin
Linezolid Penicillin
Oxacillin Ciproloxacin
Rifampicin Quinupristin-dalfopristin
Sulisoxazole Tetracycline
Trimethoprim Antimicrobial classes
Aminoglycosides Amphenicols
Carbapenems Cephalosporins II
Cephalosporins III Cephalosporins IV
Glycopeptides Glycylcyclines
Lincosamides Lipopeptides
Macrolides Nitrofurans
Oxazolidinones Penicillins
Polymyxins Quinolones
Rifamycins Streptogramins
Sulfonamides
x
Tetracyclines Trimethoprim
x
Antimicrobials italicized are second priorit y.
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1.7.1 Minimal data elements
The elements to be collected in a programme of integrated surveillance of antimicrobial resistance in foodborne bacteria should reflect the specific scientific and public health objectives,
and should take into account the feasibility of consistent collection of the desired fields. Consequently, it is not possible to define a single universal list of minimal data elements.
However, this section presents items that can serve as a basis for consideration by programme directors and data managers. In many instances, data are entered manually into the surveillance
data management system. In other instances, a laboratory may already have a data management system or laboratory instrument system for recording test results. In that case, electronic
transfer of results from the routine data management system to the surveillance system is highly recommended, in order to avoid time-consuming and error-prone manual re-entry of existing
electronic data. Irrespective of the source of a sample, the following data elements would be useful for inclusion in the surveillance protocol and database design: 1 sample information:
common sample identifier, date of sample collection, type of sample, basic epidemiological data, geographic site of collection; 2 culture results: microbial species identification, and,
where relevant, serotype; 3 antimicrobial susceptibility test results: antimicrobials tested, susceptibility test methods, quantitative susceptibility test results, and qualitative test
interpretations such as resistant, intermediate, and susceptible; and 4 additional relevant laboratory tests performed.
While it is possible to conduct a programme of integrated surveillance of antimicrobial resistance in foodborne bacteria without quantitative test results, the scientific and epidemiological value
of the resulting data will be significantly compromised. Quantitative results give insights into the population ecology and mechanisms of resistance, as well as data quality that are not possible
with test interpretation categories of resistant, intermediate, and susceptible. Furthermore, these interpretive categories are generally determined using clinical interpretation breakpoints
rather than epidemiological cut-off values ECOFFs, which can mask significant changes in the molecular epidemiology of resistance. Clinical breakpoints may also change over time as
knowledge of treatment outcomes improve and dosages change. Long-term surveillance should not be linked to breakpoints at a given point in time, but instead, data should be re-interpreted
retrospectively as dictated by the most current interpretive criteria.
1.7.1.1 Human isolates In studies of isolates of bacteria from humans, the study population usually includes ill individuals
presenting to healthcare facilities for diagnosis and therapy. Alternatively, some special studies may focus on bacterial colonization or carriage, either in healthy individuals or in patients.
Possible data fields to be considered, including all the data previously mentioned under “sample information” are: 1 patient identifiers including medical record number, national identification
number, and patient name; 2 patient demographics such as date of birth or age, sex, race, ethnicity, or nationality; 3 patient location such as medical ward, clinic, the location where the
specimen was collected from the patient, or patient’s place of residence; and 4 clinical information such as medical diagnosis and epidemiological risk factors e.g. international travel
or food exposures.
1.7.1.2 Food-producing animal isolates Samples from food-producing animals can be collected at many points in the food production
process. Samples can be taken from healthy animals on farms or at slaughter. Animal isolates from food-producing animals may be collected from samples already being gathered to satisfy
regulatory requirements, surveillance protocols, or to diagnose sick animals. Possible data fields to be considered for inclusion are: 1 animal identification information including herd
number, pen number, and animal identification number; 2 animal demographic information
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