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NRL Campylobacter Annual Report 2011 - Department of Agriculture

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NATIONAL REFERENCE LABORATORY CAMPYLOBACTER<br />

<strong>Department</strong> <strong>of</strong> <strong>Agriculture</strong>, Food and Marine,<br />

Backweston Laboratory Complex,<br />

Celbridge,<br />

Co. Kildare.<br />

(Food, Feed and Animal Health)<br />

<strong>Annual</strong> <strong>Report</strong><br />

<strong>2011</strong>


Background<br />

In 2006 following the designation <strong>of</strong> a number <strong>of</strong> additional European Union Reference<br />

Laboratories (EURL’s) Member States (MS) were required under Article 33 <strong>of</strong> regulation<br />

882 / 2004 to designate National Reference Laboratories (<strong>NRL</strong>) for each EURL. The <strong>Department</strong>s<br />

<strong>of</strong> Health and <strong>Agriculture</strong>, Food and the Marine assigned these <strong>NRL</strong> functions to<br />

a number <strong>of</strong> laboratories within the Backweston Campus. Among the <strong>NRL</strong>’s (Food, Feed<br />

and Animal Health) at Backweston are:<br />

· <strong>NRL</strong> Salmonella<br />

· <strong>NRL</strong> <strong>Campylobacter</strong><br />

· <strong>NRL</strong> E. coli<br />

· <strong>NRL</strong> Listeria and Staphylococci<br />

· <strong>NRL</strong> Antimicrobial Resistance<br />

· <strong>NRL</strong> Parasites<br />

· <strong>NRL</strong> TSE’s<br />

In addition to testing <strong>of</strong>ficial samples additional functions <strong>of</strong> <strong>NRL</strong>’s as specified in Article<br />

33 <strong>of</strong> Regulation 882/2004 include:<br />

(a) collaborating with the EURL’s in their area <strong>of</strong> competence;<br />

(b) (b) coordinating, for their area <strong>of</strong> competence, the activities <strong>of</strong> <strong>of</strong>ficial laboratories<br />

responsible for the analysis <strong>of</strong> samples in accordance with Article 11;<br />

(c) where appropriate, organising comparative tests between the <strong>of</strong>ficial national laboratories<br />

and ensuring an appropriate follow up <strong>of</strong> such comparative testing;<br />

(d) ensuring the dissemination to the competent authority and <strong>of</strong>ficial national laboratories<br />

<strong>of</strong> information that the EURL’s supply;<br />

(e) providing scientific and technical assistance to the competent authority for the implementation<br />

<strong>of</strong> coordinated control plans adopted in accordance with Article 53.<br />

2<br />

<strong>NRL</strong> <strong>Campylobacter</strong>: ANNUAL REPORT <strong>2011</strong>


Introduction<br />

<strong>Campylobacter</strong>iosis in humans is caused by thermotolerant <strong>Campylobacter</strong> spp. and the infective dose<br />

is generally low. The species most commonly associated with human infection is C. jejuni, followed<br />

by C. coli, and C. lari. The incubation period in humans averages from two to five days. Patients may<br />

experience mild to severe symptoms, with common clinical symptoms including watery, sometimes<br />

bloody diarrhoea, abdominal pain, fever, headache and nausea. Usually, infections are self-limiting<br />

and last only a few days. Infrequently, extra intestinal infections or post-infection complications such<br />

as reactive arthritis and neurological disorders occur. C. jejuni has become the most recognised antecedent<br />

cause <strong>of</strong> Guillain-Barré syndrome, a polio-like form <strong>of</strong> paralysis that can result in respiratory failure<br />

and severe neurological dysfunction and even death (EFSA <strong>2011</strong>).<br />

<strong>Campylobacter</strong> spp. are widespread in nature. The principal reservoirs are the alimentary tract <strong>of</strong> wild<br />

and domesticated birds and mammals. They are prevalent in food animals, such as poultry, cattle, pigs<br />

and sheep, in pets, including cats and dogs, in wild birds and in environmental water sources. Animals,<br />

however, rarely succumb to disease caused by these organisms. The bacteria can readily contaminate<br />

various foodstuffs, including meat, raw milk and dairy products and less frequently fish and fishery<br />

products, mussels and fresh vegetables. Among sporadic human cases, contact with live poultry, consumption<br />

<strong>of</strong> poultry meat, drinking water from untreated water sources and contact with pets and other<br />

animals have been identified as the major sources <strong>of</strong> infections. Cross contamination during foodpreparation<br />

in the home has also been described as an important transmission route. Raw milk and<br />

contaminated drinking water have been causes <strong>of</strong> large outbreaks (EFSA <strong>2011</strong>).<br />

According to the latest Community Summary <strong>Report</strong> on Trends and Sources <strong>of</strong> Zoonoses and Zoonotic<br />

Agents and Food-borne Outbreaks in the European Union (2010), campylobacteriosis was for the<br />

sixth consecutive year the most frequently reported bacterial zoonotic diseases in humans with<br />

212,064 confirmed cases in 2010 and 266 deaths. The number <strong>of</strong> reported cases increased by 6.7 % in<br />

2010 compared with 2009. The EU average notification rate was 48.6 cases per 100,000, but it was<br />

very variable between MS (Table 1).<br />

Table 1. <strong>Report</strong>ed campylobacteriosis cases in humans and notification rate in some Member<br />

States in 2010 (EFSA / ECDC)<br />

Country Confirmed Cases Cases/100,000<br />

Ireland 1,660 37.15<br />

Sweden 8,001 85.66<br />

Czech Republic 21,075 200.58<br />

United Kingdom 70,298 113.37<br />

France 4,324 6.68<br />

Spain 6,340 55.14<br />

Germany 65,110 79.59<br />

Italy 457 0.76<br />

Netherlands 3,983 46.21<br />

Denmark 4,037 72.94<br />

EU Total 212,064 48.56<br />

3


The most frequently reported <strong>Campylobacter</strong> species in 2010 was C. jejuni which accounted for<br />

93.4% <strong>of</strong> the confirmed cases characterised at the species level, it was followed by C. coli (2.3%), C.<br />

lari (0.22%) and C. upsaliensis (0.006%).<br />

Most <strong>of</strong> the test information reported on <strong>Campylobacter</strong> in foodstuffs relates to broiler meat and products<br />

there<strong>of</strong>. At EU level, 29.6% <strong>of</strong> fresh broiler meat units were found positive for <strong>Campylobacter</strong>,<br />

varying from 3.1% to 90.0% among reporting MS. In fresh turkey meat, 29.5% <strong>of</strong> tested units were<br />

found positive for the organism. In samples <strong>of</strong> fresh pig meat and bovine meat, <strong>Campylobacter</strong> was<br />

detected less frequently at levels <strong>of</strong> 0.6% and 0.4%, respectively. <strong>Campylobacter</strong> was detected in other<br />

foodstuffs only occasionally, including some findings in milk from cows and cheeses.<br />

In 2010, the proportion <strong>of</strong> <strong>Campylobacter</strong>-positive broiler flocks was 18.2% ranging from 0% to<br />

92.9% among MSs. In the case <strong>of</strong> pigs and cattle, fewer MSs provided data, but on average 34.8% <strong>of</strong><br />

pigs and 51.2% <strong>of</strong> pig herds tested positive, while the corresponding figures for cattle were 6.2% and<br />

24.3%.<br />

<strong>Campylobacter</strong> was reported as the third causative agent <strong>of</strong> food-borne outbreaks after Salmonella and<br />

viruses, with 470 reported outbreaks, i.e. 8.9%% <strong>of</strong> all reported outbreaks. There was a large variation<br />

in human infections resulting from outbreaks in the different MS, ranging from


Table 2: Results <strong>of</strong> <strong>of</strong>ficial <strong>Campylobacter</strong> tests undertaken by the Veterinary Public Health<br />

Regulatory Laboratory in chilled meat products in <strong>2011</strong><br />

<strong>Campylobacter</strong> in Food Samples tested by Food Business Operators (FBO’s) as reported to the<br />

<strong>NRL</strong><br />

Private laboratories, providing microbiological testing for FBO’s regulated by the DAFM in Ireland,<br />

submit information on <strong>Campylobacter</strong> testing undertaken to the <strong>NRL</strong> on a monthly basis. Table 3<br />

shows results <strong>of</strong> the tests undertaken in <strong>2011</strong>.<br />

Table 3: Results <strong>of</strong> <strong>Campylobacter</strong> tests undertaken by the Private Laboratories for FBO’s<br />

Type <strong>of</strong> Processing<br />

Type <strong>of</strong> Processing<br />

Abattoir Survey <strong>of</strong> <strong>Campylobacter</strong> in poultry flocks<br />

In <strong>2011</strong> a limited survey was undertaken to ascertain <strong>Campylobacter</strong> levels in poultry processed at 8<br />

abattoirs. A total <strong>of</strong> 229 submissions were received at the <strong>NRL</strong> from 167 flocks. Each submission consisted<br />

<strong>of</strong> 10 caeca plus 3 neck flaps from the same flock. The submissions were collected from 205<br />

broiler flocks, 6 duck flocks and 18 hen flocks. For testing, the contents <strong>of</strong> the 10 caeca were pooled<br />

5<br />

No. samples<br />

tested<br />

Porcine Ready to Eat (RTE) 83<br />

Porcine Cooked non RTE 53<br />

Poultry RTE 57<br />

Poultry Cooked non RTE 45<br />

Poultry processing not specified 8<br />

Porcine/poultry RTE 11<br />

No. samples tested<br />

No. samples positive<br />

Cooked meat and cooked meat products 1064 0<br />

Raw meat and raw meat products<br />

Bovine 87 0<br />

Chicken 445 150<br />

Turkey 134 87<br />

Porcine 21 0<br />

Ovine 9 0


together and mixed to constitute one sample, and the 3 neck flaps were tested together as one sample.<br />

<strong>Campylobacter</strong> detection was undertaken on 189 <strong>of</strong> the caeca samples while <strong>Campylobacter</strong> enumeration<br />

was undertaken on 73 paired caeca and neck flap (Table 2).<br />

The neck flap samples were also tested for Salmonella and the results reported in the <strong>2011</strong> <strong>NRL</strong> Salmonella<br />

<strong>Annual</strong> <strong>Report</strong> (http://www.agriculture.gov.ie/media/migration/animalhealthwelfare/<br />

labservice/nrl/<strong>NRL</strong>Salmonella<strong>Annual</strong><strong>Report</strong><strong>2011</strong>.pdf).<br />

Qualitative results<br />

For the purpose <strong>of</strong> a qualitative analysis <strong>of</strong> the results, the enumeration results have been interpreted as<br />

negative or positive, i.e. negative when no <strong>Campylobacter</strong> was isolated and positive when <strong>Campylobacter</strong><br />

was isolated from the sample regardless <strong>of</strong> the level. The level <strong>of</strong> detection set was 4 log10 cfu/g<br />

for caeca and 2 log10/g for neck flaps.<br />

A total <strong>of</strong> 156 (82.5%) <strong>of</strong> the 189 samples caecal samples tested for detection and 62 <strong>of</strong> the 73 tested<br />

for enumeration (84.9%) were positive. When the results <strong>of</strong> both detection and enumeration were combined<br />

the overall <strong>Campylobacter</strong> prevalence in caeca was 82.9%. This is similar to the 83% prevalence<br />

found in broiler caeca in the 2008 EU baseline study.<br />

There was a very high correlation, 97.0%, between detection and enumeration results in the caeca<br />

samples and there was only one sample having a different result, i.e. <strong>Campylobacter</strong> positive by the<br />

detection method but not by the enumeration method. This discrepancy could be explained by this<br />

sample having <strong>Campylobacter</strong> at a level <strong>of</strong> lower than the limit set for enumeration.<br />

Regarding the results <strong>of</strong> the neck flap samples, there were 56 positive neck flap samples out <strong>of</strong> 73<br />

samples tested, i.e. 76.7%. However this result underestimates the real prevalence <strong>of</strong> positive neck flap<br />

samples as the level <strong>of</strong> detection in neck flaps was set too high at the beginning <strong>of</strong> the study i.e. at 2<br />

log10 cfu/g. Testing these samples in previous years showed prevalence’s <strong>of</strong> 97.5% in 2008, 83.0%<br />

in 2009 and 73.0% in 2010 .<br />

An 83% correlation was observed in results between caeca and neck flap samples from the same flock.<br />

There was a statistically significant (p


Enumeration <strong>of</strong> <strong>Campylobacter</strong> in paired caeca and neck flap samples<br />

Enumeration <strong>of</strong> <strong>Campylobacter</strong> was undertaken on 73 pairs <strong>of</strong> caeca and neck flaps. Most (92.0%) <strong>of</strong><br />

the positive caeca samples had counts between 6 and 9 log10 cfu/g; with only 3.2% <strong>of</strong> positive samples<br />

reaching levels above 9 log10 cfu/g (Figure 1). Among the neck flap samples, 84.2% <strong>of</strong> those positive<br />

had levels between 2 and 4 log10 cfu/g; with only 7% <strong>of</strong> samples exceeding 4 log10 cfu/g (Figure 2).<br />

More than half <strong>of</strong> positive neck flap samples (n=32) had levels <strong>of</strong> more than 3 log10 cfu/g (43.8% <strong>of</strong><br />

the total <strong>of</strong> neck flap samples).<br />

Figure 1: Enumeration results in caeca and corresponding results in neck flaps<br />

Figure 2: Levels in neck flaps (x-axis) and corresponding levels in caeca<br />

No. submissions<br />

No. submissions<br />

25<br />

20<br />

15<br />

10<br />

30<br />

25<br />

20<br />

15<br />

10<br />

5<br />

0<br />

5<br />

0<br />


high counts in neck flaps or vice versa. It was concluded that <strong>Campylobacter</strong> levels in neck flaps could<br />

not be extrapolated from levels present in the caeca.<br />

Figure 3: Plot <strong>of</strong> enumeration results in caeca and neck flap paired samples. Results below the<br />

limit <strong>of</strong> detection have been equated to zero<br />

Differences among producers and abattoirs<br />

There was an average <strong>of</strong> 1.4 submissions per grower in this study and 88.0% <strong>of</strong> growers had at least<br />

one positive flock. There were only 20 growers that obtained negative results for <strong>Campylobacter</strong>;<br />

however these 20 growers had only one submission each. There were no major differences in the results<br />

obtained from different abattoirs with the exception <strong>of</strong> Abattoir D where a lower proportion <strong>of</strong><br />

positive caeca and neck flap samples were recorded.<br />

Figure 4: Percentage <strong>of</strong> positive growers, caeca samples and neck flap samples among different<br />

abattoirs<br />

100<br />

90<br />

80<br />

70<br />

60<br />

50<br />

40<br />

30<br />

20<br />

10<br />

0<br />

Log10 levels in neck flaps<br />

6<br />

5<br />

4<br />

3<br />

2<br />

1<br />

0<br />

y = 0.3285x + 0.1714<br />

R² = 0.3736<br />

0 2 4 6 8 10<br />

Log10 levels in caeca<br />

A B C D E F G Total<br />

8<br />

% pos growers<br />

% pos caeca samples<br />

% pos NF


Results for the present study were compared with those found on the EU broiler baseline study <strong>of</strong><br />

<strong>Campylobacter</strong> in 2008. For the four abattoirs sampled in the 2008 baseline study the percentage <strong>of</strong><br />

positive caeca were similar for both 2008 and <strong>2011</strong> results. Results <strong>of</strong> <strong>Campylobacter</strong> testing <strong>of</strong> neck<br />

flaps were more variable with Table 5 showing results <strong>of</strong> tests at the <strong>NRL</strong> from samples collected<br />

from 7 abattoirs over a four year period.<br />

Table 5: Percentage <strong>of</strong> positive neck flap samples from 7 abattoirs over a four-year period<br />

The analysis <strong>of</strong> the quantitative results obtained in the enumeration tests in the set <strong>of</strong> 73 paired caeca<br />

and neck flap samples demonstrated differences among producers (Figures 5 and 6), which were especially<br />

evident in the neck flap levels. Poultry slaughtered in Abattoir A showed the highest prevalence<br />

<strong>of</strong> <strong>Campylobacter</strong>, while Abattoir D showed lower levels in caeca and in neck flaps.<br />

100%<br />

90%<br />

80%<br />

70%<br />

60%<br />

50%<br />

40%<br />

30%<br />

20%<br />

10%<br />

0%<br />

2008 2009 2010 <strong>2011</strong><br />

A 97.4 96.43 90.62 100<br />

B 98.4 75.00 60.34 80.8<br />

C 100 78.57 55.0 80.0<br />

D None tested 89.65 68.75 57.1<br />

E 94.6 89.66 91.43 72.2<br />

F None tested 85.71 57.14 60<br />

G None tested 71.43 76.47 100<br />

Total 97.5 82.98 73.00 76.7<br />

Figure 5: Enumeration <strong>of</strong> <strong>Campylobacter</strong> in caeca from different abattoirs<br />

A B C D E F G<br />

9<br />

Caeca levels<br />

9 - 10 log10<br />

8 - 7 log10<br />

7 - 8 log10<br />

6 - 7 log10<br />

5 - 6 log10<br />


100%<br />

90%<br />

80%<br />

70%<br />

60%<br />

50%<br />

40%<br />

30%<br />

20%<br />

10%<br />

0%<br />

Figure 6: Enumeration <strong>of</strong> <strong>Campylobacter</strong> in neck flaps from different abattoirs<br />

A B C D E F G<br />

Effect <strong>of</strong> thinning flocks on <strong>Campylobacter</strong> prevalence<br />

There were 91 flocks thinned, 60 not thinned and 78 <strong>of</strong> unknown status. The percentage <strong>of</strong> positive<br />

caeca was higher for thinned flocks (91.2%) compared to the “not thinned” flocks (71.7%).<br />

Effect <strong>of</strong> killing age on <strong>Campylobacter</strong> prevalence<br />

The effects <strong>of</strong> age at slaughter on both the prevalence and levels <strong>of</strong> <strong>Campylobacter</strong> are shown in Figures<br />

7 and 8. Results show that birds get colonised as they get older, but once colonised peak counts<br />

are reached in a short space <strong>of</strong> time.<br />

Figure 7: Correlation between the killing age <strong>of</strong> the birds and the counts obtained in the caeca<br />

samples<br />

Log10 count at caeca<br />

10<br />

9<br />

8<br />

7<br />

6<br />

5<br />

4<br />

3<br />

2<br />

1<br />

10<br />

y = 0.11x + 2.5236<br />

R² = 0.0369<br />

0<br />

30 35 40 45 50<br />

Killing age <strong>of</strong> bird<br />

Neck flap levels<br />

5 - 6 log10<br />

4 - 5 log10<br />

3 - 4 log10<br />

2 - 3 log10<br />


No. birds<br />

Figure 8: Number <strong>of</strong> negative and positive birds distributed by killing age <strong>of</strong> birds<br />

35<br />

30<br />

25<br />

20<br />

15<br />

10<br />

5<br />

0<br />

<strong>Campylobacter</strong> species<br />

29 30 31 32 33 34 35 36 37 38 38 39 40 41 42 43 44 46 46 47 49 56 57 58<br />

Killing age <strong>of</strong> bird<br />

Speciation <strong>of</strong> <strong>Campylobacter</strong> was carried out by PCR. <strong>Campylobacter</strong> jejuni was the most frequently<br />

isolated species, 66.3%, compared to C. coli, 24.3%. Mixed C. jejuni and C. coli were identified in<br />

6.7% <strong>of</strong> isolates analysed. Only 1 C. lari was encountered (Figure 9).<br />

Figure 9: Breakdown <strong>of</strong> <strong>Campylobacter</strong> species<br />

Speciation <strong>of</strong> <strong>Campylobacter</strong> for FSAI surveillance<br />

The <strong>NRL</strong> undertook speciation <strong>of</strong> isolates received as part <strong>of</strong> an FSAI survey on <strong>Campylobacter</strong> in<br />

poultry meats at retail. A total <strong>of</strong> 323 isolates were speciated and the results showed that 75% <strong>of</strong> isolates<br />

were C. jejuni and 20% were C. coli (Figure 10).<br />

11<br />

Negative<br />

Positive


Figure 10: Breakdown <strong>of</strong> <strong>Campylobacter</strong> species in strains from an FSAI survey<br />

<strong>Campylobacter</strong> in Diagnostic samples<br />

A total <strong>of</strong> 4,738 diagnostic samples received at the Regional Veterinary Laboratories (RVL’s) were<br />

tested for <strong>Campylobacter</strong> spp. Results <strong>of</strong> some tests are shown in Table 6.<br />

Table 6: <strong>Campylobacter</strong> isolations from some diagnostic samples at the RVL’s in <strong>2011</strong><br />

<strong>Campylobacter</strong> spp<br />

Bovine genital campylobacteriosis<br />

Bovine genital campylobacteriosis is a venereal disease <strong>of</strong> cattle caused by <strong>Campylobacter</strong> fetus venerealis<br />

or C. fetus fetus. Infection is characterized primarily by early embryonic death, infertility, a protracted<br />

calving season, and occasionally abortion. The organisms are transmitted venereally and also<br />

by contaminated instruments, bedding, or by artificial insemination using contaminated semen. Individual<br />

bulls vary in their susceptibility to infection; some become permanent carriers, while others<br />

appear to be resistant to infection.<br />

A total <strong>of</strong> 209 samples were tested at the RVL’s during <strong>2011</strong>. None were found positive.<br />

Antimicrobial resistance in <strong>Campylobacter</strong> isolates from poultry<br />

Details <strong>of</strong> antimicrobial resistance testing for <strong>Campylobacter</strong> in <strong>2011</strong> are presented in the <strong>NRL</strong> AMR<br />

<strong>Annual</strong> <strong>Report</strong> available on the DAFM website http://www.agriculture.gov.ie/media/migration/<br />

animalhealthwelfare/labservice/nrl/<strong>Annual</strong><strong>Report</strong><strong>2011</strong><strong>NRL</strong>AMR310712.pdf<br />

12<br />

C. jejuni<br />

C. coli<br />

Mixed C. jejuni and C.coli<br />

C. lari<br />

<strong>Campylobacter</strong> spp. other<br />

than jejuni, coli or lari<br />

Mixed C. Jejuni and C. Lari<br />

Bovine Ovine Porcine Equine<br />

270/3229<br />

14/845<br />

1/25<br />

0/6


In summary a total <strong>of</strong> 119 strains <strong>of</strong> C. jejuni and 44 <strong>of</strong> C. coli isolated from poultry caeca were tested<br />

for antimicrobial susceptibility in <strong>2011</strong>. Results indicated that resistance levels were higher in C. jejuni<br />

than in C. coli, with 64.7% and 59.1% <strong>of</strong> strains found resistant respectively. High levels <strong>of</strong> resistance<br />

were observed towards cipr<strong>of</strong>loxacin, nalidixic acid, and tetracycline. Resistance to streptomycin and<br />

erythromycin was seen in few isolates and all were susceptible to gentamicin and chloramphenicol.<br />

A comparison <strong>of</strong> the levels <strong>of</strong> resistance to different antimicrobials observed from 2008 to <strong>2011</strong><br />

(Figure 11) showed that levels <strong>of</strong> resistance have increased substantially for quinolones in both C.<br />

jejuni and C. coli, and for tetracycline among C. coli. The level <strong>of</strong> streptomycin resistance has decreased<br />

slightly.<br />

Figure 11: Trends on resistance levels to tested antimicrobials from 2008 (point 1) to <strong>2011</strong> (point<br />

4) in <strong>Campylobacter</strong> jejuni (top chart) and <strong>Campylobacter</strong> coli (bottom chart)<br />

60<br />

50<br />

40<br />

30<br />

20<br />

10<br />

60<br />

50<br />

40<br />

30<br />

20<br />

10<br />

0<br />

0<br />

1 2 3 4<br />

1 2 3 4<br />

13<br />

Tetracycline<br />

Cipr<strong>of</strong>loxacin<br />

Nalidixic acid<br />

Streptomycin<br />

Erythromycin<br />

Gentamycin<br />

Chloramphenicol<br />

Cipr<strong>of</strong>loxacin<br />

Nalidixic acid<br />

Tetracycline<br />

Streptomycin<br />

Erythromycin<br />

Gentamycin<br />

Chloramphenicol


Summary points<br />

1. The percentage <strong>of</strong> <strong>Campylobacter</strong> positive poultry flocks and poultry meat samples remain<br />

similar levels to those found in the 2008 baseline survey.<br />

2. There is a significant correlation between positive flocks and positive neck flap samples.<br />

3. In the event that targets levels for <strong>Campylobacter</strong> are considered the data presented in this report<br />

might serve as a useful guide. Most positive flocks have counts between 6 and 9 log10 cfu/g; with<br />

only 3.2% <strong>of</strong> positive samples reaching levels above 9 log10 cfu/g. Most <strong>of</strong> the positive neck flaps have<br />

levels between 2 and 4 log10 cfu/g; with only 7% <strong>of</strong> samples exceeding levels <strong>of</strong> 4 log10 cfu/g. Approximately<br />

one half <strong>of</strong> neck flap samples have levels <strong>of</strong> more than 3 log10 cfu/g.<br />

4. There is an association between the killing age and <strong>Campylobacter</strong> status <strong>of</strong> flock, with a higher<br />

percentage <strong>of</strong> flocks killed late in life showing positive results. There is also an association between<br />

thinning and the presence <strong>of</strong> <strong>Campylobacter</strong> in caeca.<br />

5. One abattoir showed a significantly lower percentage <strong>of</strong> positive flocks in its suppliers and also<br />

lower <strong>Campylobacter</strong> counts in positive samples.<br />

Quality Manager: Don O’Grady, MSc<br />

Tel: 353 1 6157148<br />

Fax: 353 1 6157116<br />

Email: don.ogrady@agriculture.gov.ie<br />

Technical Manager: Montserrat Gutierrez, DVM, PhD<br />

Tel: 353 1 6157222<br />

Fax: 353 1 6157116<br />

Email: mm.gutierrez@agriculture.gov.ie<br />

<strong>NRL</strong> Contact & Head Division: John Egan, MVB, MVM, PhD, FRCVS<br />

Tel: 353 1 6157138<br />

Fax: 353 1 6157116<br />

Email: john.egan@agriculture.gov.ie<br />

14


Molecular subtyping <strong>of</strong> <strong>Campylobacter</strong> jejuni and <strong>Campylobacter</strong> coli isolated<br />

from Irish poultry<br />

Deirdre M Prendergast 1 , Eadaoίn Nί Ghallchóir 1 , Margaret Griffin 1 , Frances Colles 2 , Martin<br />

CJ Maiden 2 , John Egan 1 and Montserrat Gutierrez 1<br />

1 National Reference Laboratory for <strong>Campylobacter</strong>, Backweston Complex, Celbridge, Co. Kildare, Ireland. 2 <strong>Department</strong> <strong>of</strong> Zoology, University <strong>of</strong> Oxford, South Parks Road, OX1 3PS, UK<br />

Introduction<br />

<strong>Campylobacter</strong>iosis represents the most frequently reported disease in humans in the European Union (EU). Human infections are most <strong>of</strong>ten due<br />

to consumption <strong>of</strong> undercooked or cross contaminated poultry products (Moore et al. 2005). Because C. jejuni and C. coli are ubiquitous in<br />

animals, foods and the environment, this makes it difficult to study the cause, distribution and control <strong>of</strong> human campylobacteriosis. Molecular<br />

subytping is not only necessary for outbreak investigation but also critical in determining the source <strong>of</strong> foodborne illness and to monitor the<br />

spread <strong>of</strong> resistant strains (Wassenaar et al. 2000; Wang et al. <strong>2011</strong>). Over the last decade, multi locus sequence typing (MLST) has been<br />

considered the most suitable method <strong>of</strong> choice. The main advantage <strong>of</strong> MLST over pulsed field gel electrophoresis (PFGE) is the standardised<br />

nomenclature and the ability to easily transfer and compare results between laboratories (De Haan et al. 2010).<br />

This study used two molecular subtyping methods i.e., PFGE and the high resolution 10-locus typing scheme (Dingle et al. 2008) which includes<br />

MLST and nucleotide sequence typing <strong>of</strong> the flaA, flaB and MOMP to characterise C. jejuni and C. coli isolated from caeca, carcass swabs and boot<br />

covers at nine different Irish poultry plants during 2008 to 2010.<br />

Methods<br />

A representative number <strong>of</strong> isolates were chosen from our collection: 118 C. jejuni<br />

and 69 C. coli isolates from caeca and neck flaps sampled at nine different Irish<br />

poultry plants during 2008-2010. Isolates had been previously speciated by PCR.<br />

All cultures were stored on beads at -80 o C. These beads were streaked over<br />

nutrient agar (NA) and blood agar and incubated in a microaerobic atmosphere for<br />

48 h at 41.5 o C. DNA was extracted from cultures on NA using InstaGene (BioRad)<br />

and extracted DNA was used for MLST and nucleotide sequencing typing <strong>of</strong> the flaA,<br />

flaB and MOMP (Dingle et al. 2008). PFGE was performed on cultures from blood<br />

agar following the PulseNet protocol for <strong>Campylobacter</strong>. PFGE images were<br />

analysed using the fingerprint analysis s<strong>of</strong>tware in BioNumerics (version 6.5;<br />

Applied Maths, Saint-Martens-Latem, Belgium). A dendrogram was constructed<br />

using the band-based dice similarity coefficient and the unweighted pair’s<br />

geometric matched analysis (UPGMA) with a position tolerance setting <strong>of</strong> 1.5% for<br />

optimisation and position tolerance <strong>of</strong> 1.5% for band comparison. MLST and<br />

nucleotide sequence results were imported as character data into the same<br />

database for analysis and comparison with the PFGE results.<br />

Results<br />

Figure 1. MLST and nucleotide sequence typing (flaA) <strong>of</strong> C.<br />

jejuni CC-45<br />

PFGE<br />

The C. jejuni and C. coli isolates were not grouped together. Analysis <strong>of</strong> the 118 C. jejuni<br />

isolates by PFGE revealed common patterns, and allowed grouping into 48 clusters based on a<br />

genetic relatedness criterion <strong>of</strong> 90%. The 69 C. coli isolates were grouped into 23 PFGE clusters.<br />

When the 26 C. jejuni isolates with ST-45 were analysed by PFGE, SmaI patterns displayed<br />

between 1 and 13 bands (Figure 2). These 26 isolates were grouped into 8 different clusters<br />

based on a genetic relatedness <strong>of</strong> 90% (Figure 2).<br />

Discussion<br />

This study revealed a high diversity <strong>of</strong> MLSTs among the 118 C. jejuni and 69 C. coli<br />

investigated. The additional nucleotide sequencing provided further discrimination. MLST<br />

showed that C. jejuni were more diverse than C. coli with all but one C. coli belonging to the<br />

same CC-828, similar findings have been reported in other studies. While the use <strong>of</strong> flaA alone<br />

may lack sufficient discrimination, it further differentiated among strains belonging to identical<br />

MLST types. PFGE separated C. jejuni and C. coli into two distinct groups and proved highly<br />

discriminatory within each species. When examined together, MLST, flaA and PFGE results were<br />

not fully comparable, as presented in our results.<br />

In some cases, the use <strong>of</strong> MLST and PFGE demonstrated relatedness among strains that<br />

originated from the same location, which indicated persistent contamination.<br />

References<br />

MLST<br />

flaA<br />

MLST<br />

The distribution <strong>of</strong> multilocus sequence types among poultry C. jejuni and C.<br />

coli isolates during 2008 to 2010 is presented in Table 1. Among the 118 C.<br />

jejuni and 69 C. coli investigated, a total <strong>of</strong> 13 clonal complexes (CCs) and 29<br />

sequence types (STs) were observed for C. jejuni and a total <strong>of</strong> 2 CCs and 23<br />

STs were observed for C. coli. Seventeen C. jejuni and 7 C. coli isolates did not<br />

have a complete pr<strong>of</strong>ile and were therefore not assigned a CC (Table 1). The<br />

most common CC observed in C. jejuni isolates was CC-45 (26 isolates).<br />

Within CC-45, 7 STs were observed and ST-45 was the most common (Figure<br />

1). Nucleotide sequence typing <strong>of</strong> the flaA, flaB and MOMP provided additional<br />

discrimination for example, flaA further discriminated ST-45 to include 7<br />

different flaA types (Figure 1). The most prevalent CC observed in C. coli was<br />

828 (54 isolates).<br />

De Haan, C.P.A., Kivistö, R.I., Hakkinen, M., Corander, J., Hänninen, M.L. (2010) Multilocus sequence types <strong>of</strong> finnish bovine <strong>Campylobacter</strong> jejuni isolates and their attribution to human infections.<br />

BMC Microbiology, 10:200.<br />

Dingle, K.E., McCarthy, N.D., Cody, A.J., Peto, T.E.A. and Maiden, M.C.J. (2008). Extended sequence typing <strong>of</strong> <strong>Campylobacter</strong> spp., United Kingdom, Emerging Infectious Diseases, 14, 1620-1622.<br />

Moore, J.E., Corcoran, D., Dooley, J.S.G., Fanning, S., Lucey, B., Matsuda, M., McDowell, D.A., Mégraud, F., Millar, B.C., O’ Mahony, R., O’ Riordan, L., O’ Rourke, M., Rao, J.R., Rooney, P.J., Sails, A.<br />

and Whyte, P. (2005) <strong>Campylobacter</strong> Vet. Res. 36, 351-382.<br />

Wang, X., Zhao, S., Harbottle, H., Tran, T., Blickenstaff, K., Abbott, J. and Meng, J. (<strong>2011</strong>) Antimicrobial resistance and molecular subtyping <strong>of</strong> <strong>Campylobacter</strong> jejuni and <strong>Campylobacter</strong> coli from<br />

retail meats. Journal <strong>of</strong> Food Protection, 74, 616-621.<br />

15<br />

Table 1. Distribution <strong>of</strong> MLST among poultry C. jejuni and C.<br />

coli isolates from 2008 to 2010.<br />

Species Clonal complex No. <strong>of</strong> STs No. <strong>of</strong> isolates<br />

C. jejuni 45 7 26<br />

661 3 25<br />

257 1 16<br />

21 4 9<br />

42 3 7<br />

460 1 5<br />

353 3 3<br />

52 1 3<br />

443 1 2<br />

48 2 2<br />

1332 1 1<br />

206 1 1<br />

607 1 1<br />

Not assigned 6 17<br />

Total no.<br />

118<br />

C. coli 1150 1 2<br />

828 15 54<br />

Not assigned 7 13<br />

Total no.<br />

69<br />

Figure 2. PFGE analysis <strong>of</strong> C. jejuni CC-45 isolates

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