Genetic diversity of Mycobacterium avium subspecies paratuberculosis isolates from goats detected by pulsed-field gel electrophoresis

Paratuberculosis in goats occurs worldwide causing considerable economic losses mainly due to reduced milk production. Nowadays, there is still relatively little knowledge about the epidemiology of this disease in goats, and only a few epidemiological studies have been carried out in goats naturally infected with Mycobacterium avium subspecies paratuberculosis (M. a. paratuberculosis). The objective of this study was to characterize forty four clinical caprine isolates of M. a. paratuberculosis by different molecular techniques (pulsed-field gel electrophoresis [PFGE], restriction fragment length polymorphism analysis coupled with hybridization to IS900, and IS1311 polymerase chain reaction-restriction enzyme analysis) to determine the most useful technique for molecular typing of caprine isolates, as well as to disclose the genetic variation amongst caprine isolates and the relationship with strains isolated from other animal species. PFGE was found to be the most discriminative technique identifying a total of 13 'multiplex' PFGE profiles, ten of which were novel profiles found only in caprine isolates to date. All isolates were genotyped as Type II strains, except two isolates that resembled the intermediate group referred as Type III.     

Demonstration of polymorphism among Brucella ovis field isolates by pulsed-field gel electrophoresis

Brucella ovis is recognized worldwide as an important pathogen of sheep, and has also been identified in farmed deer in New Zealand. Previously, only one strain type of B. ovis has been identified. The objective of this paper was to perform pulsed-field gel electrophoresis (PFGE) on field isolates of B. ovis to determine whether strain variations exist, whether sheep and deer are affected by the same strains, and to compare the performance of the rare-cutting restriction enzymes XbaI and SwaI. Ten B. ovis isolates from sheep and two from deer in New Zealand, as well as the type strain, were subjected to PFGE analysis using both XbaI and SwaI. PFGE of XbaI restriction fragments produced two banding patterns consisting of 27-28 bands, which were found to be 98% similar by cluster analysis, and were named X1 and X1a. PFGE of SwaI restriction fragments resulted in three banding patterns consisting of 13-15 bands each. Ten of the isolates had identical banding patterns and were named S1. One isolate differed by one band, representing a subtype named S1a. Two isolates differed by six bands, representing a different strain type of B. ovis and this was named S2. Cluster analysis showed S2 to be 78% similar to the S1/S1a cluster. Both strain types were isolated from both sheep and deer. Thus, two distinct strain types of B. ovis were identified in New Zealand, which is the first report of more than one strain type being identified worldwide. Neither strain was species-specific for sheep or deer. The restriction endonuclease SwaI was found to be more discriminatory than the enzyme XbaI, which has been used in previous studies.     

Genomic diversity of Bartonella henselae isolates from domestic cats from Japan, the USA and France by pulsed-field gel electrophoresis

The genomic DNA diversity of 27 Bartonella henselae and three B. clarridgeiae isolates from 18 domestic cats from Japan, the USA and France was investigated by pulsed-field gel electrophoresis (PFGE) with NotI, AscI and SmaI restriction enzymes. A great diversity of genomic patterns was found for all B. henselae, but none for B. clarridgeiae isolates. The DNA size of B. henselae and B. clarridgeiae isolates were 1.7-2.9 and 1.7Mbp, respectively. All 13 Japanese cat isolates were identified as B. henselae type I. Furthermore, three of the four Japanese cats harbored genetically different B. henselae type I isolates, suggesting for the first time co-infection with various type I isolates.One French cat and one American cat were co-infected with B. henselae and B. clarridgeiae. B. henselae type I and type II were mainly grouped in two different clusters by PFGE using SmaI endonuclease in the dendrogram.     

Comparison of Pseudomonas aeruginosa isolates from mink by serotyping and pulsed-field gel electrophoresis

Isolates of Pseudomonas aeruginosa from clinical infections in mink were subjected to serotyping and pulsed-field gel electrophoresis (PFGE) using SpeI. A total of 212 isolates of P. aeruginosa from the year 1998 to 2001 were included in this study: 168 isolates from mink obtained from 74 farm outbreaks of haemorrhagic pneumonia. Isolates from mink were separated into 34 distinct clones by PFGE subtyping. All isolates from mink infected during the same farm outbreak were identical, except in one case where two different strains were isolated from mink obtained from the same farm outbreak. P. aeruginosa of specific PFGE types were found to cause clusters of outbreaks on several farms within a few weeks of each other. However, PFGE types of strains causing clusters of farm outbreaks changed from year to year. These results suggest that some outbreaks of haemorrhagic pneumonia are caused by pathogenic strains of P. aeruginosa spread between farms and animals either mechanically, or through feed or water from a common source, rather than by random nosocomial infections with strains from the farm environment.     

Transmission of Campylobacter spp. in a poultry slaughterhouse and genetic characterisation of the isolates by pulsed-field gel electrophoresis

1. Contamination of retail products with Campylobacter spp. during the slaughter of poultry is a well-known problem of product hygiene. Mechanical evisceration often leads to intestinal rupture and discharge of gut contents, which can contain zoonotic and human pathogens. Processes along the slaughter line cause aerosols and airborne droplets, containing bacterial loads. 2. To estimate the possible transmission routes of intestinal Campylobacter, 36 measurements of the bioaerosol (Andersen sampler and SKC BioSampler), 30 cloacal (of three flocks), 10 equipment and 4 sedimentation samples were tested for the presence of Campylobacter species. 3. The results imply that, in addition to contaminated equipment, which was Campylobacter-positive in 80% of cases, aerosols with peak values of 4.0 x 10(4) (test series 1) and 1.4 x 10(4) (test series 2) CFU/m3 also provide a potential vector for horizontal transmission. 4. To explore the genetic similarities of isolates from different origins, 18 isolates recovered from air, 26 cloacal, 8 equipment and 4 sedimentation isolates were analysed by pulsed-field gel electrophoresis (PFGE), using the restriction enzymes Sma I and Sal I. The similarity of cloacal isolates with isolates from equipment, air and sediment, suggest that the contamination is of intestinal origin. 5. There were direct links between Campylobacter-positive flocks and the presence of the same strains in the aerosol of the slaughter hall. Air as a potential source for microbial transmission must be taken into account.     

Differentiation of Australian isolates of Mycobacterium paratuberculosis using pulsed-field gel electrophoresis

Objectives To examine strain variation amongst Australian isolates of Mycobacterium paratuberculosis .
Design Pulsed field gel electrophoresis was optimised for differentiation of M paratuberculosis strains, and this typing technique was then applied to a collection of Australian isolates.
Procedure DNAs from 35 Australian isolates of M para-tuberculosis and a UK reference strain were digested with one or other of three restriction endonucleases. The banding patterns obtained after pulsed field gel electrophoresis of the DNA fragments were compared.
Results The Australian isolates were divided into two groups on the basis of their DNA banding pattern. Both were different from the UK reference strain. Seven isolates from cattle in Victoria and the Northern Territory had the same pattern as five isolates from alpacas in Victoria and Western Australia. Another 20 isolates from cattle in Victoria, Western Australia and the Northern Territory had the same pattern as isolates from two sheep and a goat in New South Wales.
Conclusion Pulsed field gel electrophoresis was a useful tool for strain typing of M paratuberculosis , and could be used to study the transmission of strains in Australia.     

Genetic diversity of Clostridium perfringens isolated from healthy broiler chickens at a commercial farm

Clostridium perfringens is an important commensal and bacterial pathogen of many animal species. It has particular significance in poultry, where it may cause necrotic enteritis. Our objective was to characterize the population diversity of C. perfringens colonizing healthy birds, and to observe how diversity changed over time. Isolates were obtained from broiler chicken cecal samples in two barns on a single farm, on days 7, 14, 22, 27, 30 and 34 of a single 42-day rearing cycle. Bacitracin was used as a feed additive in one of the barns and withdrawn from the second barn for the duration of the experiment. Each isolate was typed using pulsed-field gel electrophoresis (PFGE) using SmaI restriction endonuclease. A total of 205 cecal isolates from 49 birds were typed, as well as 93 isolates from the barn environment (bedding, drinking water and feces). Eight major PFGE types and 17 subtypes were found in the 298 total isolates. The results show that an optimal sampling strategy would involve a large number of birds, with only a few isolates sampled per bird. The diversity of C. perfringens in this study appears to be low within a single bird, and increases as the bird matures. There was no significant difference in genetic diversity between the two barns. In addition, isolates from fresh fecal samples appear to represent the cecal C. perfringens population accurately, although this was not proven statistically. Antimicrobial susceptibility testing was performed on selected isolates (n=41) representing a cross-section of PFGE types. Based on minimum inhibitory concentration distributions, 95% of the isolates tested were deemed resistant to bacitracin, with a 16 microg/mL breakpoint. Three new cpb2 (beta2 toxin gene) variants were found in the study.     

Erysipelothrix rhusiopathiae: genetic characterization of midwest US isolates and live commercial vaccines using pulsed-field gel electrophoresis.

This is the first report of molecular characterization of US erysipelas field isolates and vaccine strains of Erysipelothrix rhusiopathiae by pulsed-field gel electrophoresis (PFGE). Erysipelas in pigs is mainly caused by E. rhusiopathiae serotypes 1a, 1b, and 2. In 2001, erysipelas reemerged as a clinical problem in pigs in the midwestern United States. In this work 90 erysipelas isolates (58 recent and 28 archived field isolates as well as 4 live-vaccine strains) were genetically characterized. Because of the limited availability of antiserum, 74/90 isolates (44/58 recent isolates) were serotyped. The serotype of the majority (79.6%) of the 44 recent isolates tested was determined to be 1a, 13.6% were serotype 1b, and 6.8% of recent isolates were serologically untypeable. Among all 90 isolates, 23 different PFGE patterns were identified. There were 43 isolates identified as serotype 1a with 4 genetic patterns: 38/43, 1A(I); 3/43, 1A(III); 1/43, 1B(V); and 1/43, 3B. Sixteen serotype 1b isolates had 11 unique genetic patterns: 4/16 were genotype 1B(III), 2/16 were genotype 3A(I), and 1/16 was in genotype groups 1A(V), 1A(VI), 1A(VII), 1B(I), 1B(IV), 1B(VII), 2, 4, and 5. Six genetic patterns were distinguished among the 10 serotype 2 isolates: 1A(IV) (1/10), 1A(V) (1/10), 1B(VI) (1/10), 2 (4/10), 7 (1/10), and 8 (2/8). Erysipelas vaccine strains (modified live) were similar to each other but different from current field strains, sharing 78.6% identity with the most prevalent genotype 1A(I) based on the PFGE-SmaI pattern. Compared with serotyping, PFGE genotyping is a more distinguishing technique, easy to perform and not dependent on the limited availability of antiserum.     

Improved pulsed-field gel electrophoresis procedure for the analysis of Flavobacterium columnare isolates previously affected by DNA degradation

Flavobacterium columnare is a fresh water bacterium that causes columnaris diseases in over 36 fish species. Intra-species typing of F. columnare can be performed by pulsed-field gel electrophoresis (PFGE). However, this method is hampered by the degradation of chromosomal DNA in about 10% of strains. In the current study, DNA degradation problems caused by extracellular DNases were overcome by fixation of cells with formaldehyde prior to isolation. The results substantiate that after problems due to DNases are overcome, PFGE analysis is a reproducible highly discriminating epidemiological method for studying F. columnare isolates regardless of fish host.     

The diversity of Mycoplasma hyopneumoniae within and between herds using pulsed-field gel electrophoresis

Over the years, pulsed-field gel electrophoresis (PFGE) has been proven a robust technique to type isolates with a high resolution and a good reproducibility. In this study, a PFGE protocol is described for the typing of Mycoplasma hyopneumoniae isolates. The potential of this technique was demonstrated by comparing M. hyopneumoniae isolates obtained from the same as well as from different herds. The use of two different restriction enzymes, SalI and ApaI, was evaluated. For each enzyme, the resulting restriction profiles were clustered using the unweighted pair group method with arithmetic means (UPGMA). For both obtained dendrograms, the included isolates of the related M. flocculare species clustered separately from all M. hyopneumoniae isolates, forming the root of the dendrograms. The PFGE patterns of the M. hyopneumoniae isolates of different herds were highly diverse and clustered differently in both dendrograms, illustrated by a Pearson's correlation coefficient of only 0.33. A much higher similarity was observed with isolates originating from different pigs of a same herd. The PFGE patterns of these isolates always clustered according to their herd and this for both dendrograms. In conclusion, the results indicate a closer relationship of M. hyopneumoniae isolates within a herd compared to isolates from different herds and this for both restriction enzymes used. Since the described PFGE technique was shown to be highly discriminative and reproducible, it will be a helpful tool to further elucidate the epidemiology of M. hyopneumoniae.     

Molecular genotyping of multinational ovine and caprine Corynebacterium pseudotuberculosis isolates using pulsed-field gel electrophoresis

Caseous lymphadenitis (CLA) is a chronic, suppurative disease, with a worldwide distribution, caused by Corynebacterium pseudotuberculosis. The clinical manifestation of CLA is known to vary between different countries, and has been postulated to be due to differences in the strains present in these countries. Forty-two sheep and goat isolates of C. pseudotuberculosis from Australia, Canada, Eire, The Netherlands and Northern Ireland were characterized by pulsed-field gel electrophoresis (PFGE), biotyping, antimicrobial susceptibility, and production of phospholipase D. The PFGE-determined genotypes of this multicentric collection were then compared with representative ovine and caprine isolates from a previously published panel of PFGE profiles of United Kingdom isolates. Digestion with SfiI generated 16-18 bands in the 48.5 and 290 kb range, and differentiated four distinct pulsotypes amongst the 36 ovine and 6 caprine strains which displayed remarkable homogeneity. Based on these results, it would appear that the genome of C. pseudotuberculosis is highly conserved, irrespective of the country of strain origin.     

青岛地区兔源产气荚膜梭菌的分离鉴定及遗传多样性分析

兔的梭菌性肠炎是由产气荚膜梭菌感染引起的严重危害养兔业的一种疾病,为了更好地控制此病,本研究调查了青岛地区规模化兔场爆发此病时产气荚膜梭菌的毒素型及遗传多样性。2010年11月-2012年5月期间,采集青岛地区规模化养兔场疑似产气荚膜梭菌感染兔的肝脏进行产气荚膜梭菌的分离鉴定,采用Multiple—PCR方法对分离菌株进行毒素型分析,应用ERIC-PCR方法分析分离菌株的遗传多样性。共分离到25株产气荚膜梭菌,其中A型24株（96％）,C型1株（4％）。用ERIC—PCR方法将25株分离株分于9个聚类中,其中V型为主要流行型。结果表明：青岛地区规模化兔场中产气荚膜梭菌流行的毒素型主要为A型,且具有多种基因亚型,其中V型为主要流行型。此结果为该地区兔产气荚膜梭菌病的免疫和微生态防治提供了重要的参考依据。     

Epidemiological analysis of Salmonella enteritidis from human outbreaks by pulsed-field gel electrophoresis.

To determine the extent of genetic diversity among isolates of Salmonella enteritidis obtained from outbreaks in Fukuoka Prefecture, Japan, from 1989 to 1994, we analyzed a total of 55 isolates of S. enteritidis obtained from 13 distinct outbreaks with pulsed-field gel electrophoresis. These isolates showed three different patterns in pulsed-field profile with Bln I digestion. The groups A, B and C consisted of three outbreaks isolates (Dice coefficient, F = 1), of seven outbreaks (F = 0.56-0.94) and of three outbreaks (F = 0.65-0.78), respectively. This result suggests that a few limited clonal lines of S. enteritidis were successively causing outbreaks in this area from 1989 to 1994.     

Rapid molecular typing of Listeria monocytogenes by pulsed-field gel electrophoresis

Pulsed-field gel electrophoresis (PFGE) is a highly discriminating tool for molecular typing, but the conventional PFGE protocol is time consuming. This paper describes a rapid method of PFGE for Listeria monocytogenes that yields results within 2 days.     

Chromosome-sized DNA of Malassezia pachydermatis by pulsed-field gel electrophoresis.

The genome of Malassezia pachydermatis isolates from dogs was resolved into six chromosomes by using pulsed-field gel electrophoresis and their molecular sizes were calculated as 820, 1,100, 1,400, 1,470, 1,660 and 1,820 Kb, respectively. Comparison of electrophoretic patterns suggested that the chromosomes of M. pachydermatis were homozygous.     

Antimicrobial resistance in Clostridium perfringens isolates from broilers in Belgium

The antimicrobial susceptibility of Clostridium perfringens strains isolated from Belgian broilers between May and September 2007 was investigated. All 39 tested isolates were sensitive to enrofloxacin, erythromycin, tylosin, florfenicol and bacitracin. Twenty-six (66%) and 24 (61%) out of the 39 tested isolates showed acquired resistance to tetracycline and lincomycin, respectively. The C. perfringens isolates were also screened by PCR for the presence of the resistance genes tet(K), tet(L), tet(M), tetB(P), tet(O), tet(W), lnu(A) and lnu(B). In 22/26 tetracycline resistant strains and 7/24 lincomycin resistant strains, resistance could be attributed to one or more of these genes. An extended frequency distribution range of MICs was seen for ampicillin. These data are consistent with data derived from studies carried out in 1980 and in 2004, indicating that no changes in antimicrobial resistance patterns have taken place during time in C. perfringens isolates from broilers in Belgium.     

Genotyping of Ureaplasma diversum isolates using pulsed-field electrophoresis

Ureaplasma diversum has been associated with reproductive disorders in cattle and in the present study genotypic variations among U. diversum isolates obtained from the vaginal mucus of healthy cattle and sick animals were analyzed by enzymatic digestion and pulsed-field gel electrophoresis (PFGE). The influence of time and broth volume was important in obtaining sufficient cell sediment and DNA for PFGE. The method presented a high discriminatory power and satisfactory reproducibility for the analysis of detected variations among U. diversum isolates and strains. Different band profiles and wide genotypic heterogeneity were detected but no association between DNA polymorphism and sick or healthy animals could be established.     

Epidemiologic study of results of pulsed-field gel electrophoresis of isolates of Rhodococcus equi obtained from horses and horse farms

OBJECTIVE: To compare isolates of Rhodococcus equi on the basis of geographic source and virulence status by use of pulsed-field gel electrophoresis (PFGE). SAMPLE POPULATION: 290 isolates of R equi (218 virulent isolates from foals and 72 avirulent isolates from feces, soil, and respiratory tract samples) obtained between 1985 and 2000 from horses and horse farms from 4 countries. PROCEDURE: DNA from isolates was digested with the restriction enzyme Asel and tested by use of PFGE. Products were analyzed for similarities in banding patterns by use of dendrograms. A similarity matrix was constructed for isolates, and the matrix was tested for nonrandom distributions of similarity values with respect to groupings of interest. RESULTS: There was little grouping of isolates on the basis of country, virulence status, or region within Texas. Isolates of R equi were generally < 80% similar, as determined by use of PFGE. Isolates from the same farm generally were rarely of the same strain. CONCLUSIONS AND CLINICAL RELEVANCE: Considerable chromosomal variability exists among isolates of R equiobtained from the same farm, sites withinTexas, or among countries from various continents. Only rarely will it be possible to link infections to a given site or region on the basis of analysis of isolates by use of PFGE of chromosomal DNA.     

奶牛乳房炎金黄色葡萄球菌脉冲场凝胶电泳分型研究

为探讨新疆北疆奶牛乳房炎致病菌的流行规律,本研究采用Sma Ⅰ酶切,脉冲场凝胶电泳(PFGE)分型的方法对43株分离自新疆6个规模奶牛场隐性乳房炎奶样的金黄色葡萄球菌进行了分子分型比较研究.结果表明,所有菌株都能被PFGE法分型,43株金黄色葡萄球菌可分为A、B、C、D和E 5个基因型.A型株(22株,51.2%)有13个亚型,相似度在81.8%～96.8%之间,在5个奶牛场均分离到,是主要的流行株;B型(25.6%)、C型(14.0%)、D型(7.0%)各型别内菌株间的相似度为100%,E型仅有1株.不同地区主要流行株有差别:乌鲁木齐主要流行A型菌株,昌吉以A型和B型菌株为主,而奎屯主要流行C型和B型.有2个奶牛场流行株只有1个基因型,也有2种基因型(3个牛场)或3种基因型(1个牛场)同时存在,但以1种为优势株.这些结果提示,不同地区主要流行株有差别,多数奶牛场以1种流行株感染为主,不同牛场可能流行相同的菌株,在较大地域范围内某些流行株具有侵染优势.