Microarray-based genotyping of Staphylococcus aureus isolates from camels

Staphylococcus aureus is a common cause of mastitis and other diseases in camels. In order to obtain data on population structure as well as on the carriage of toxin genes and resistance markers, a collection of 45 isolates from dromedaries of Dubai, United Arab Emirates, were genotyped. These isolates belonged to clonal complexes CC6 (twenty isolates; 44.44%), CC30 (sixteen isolates; 35.56%), CC188 (five isolates; 11.11%), CC152 (1 isolate, 2.2%) and to a previously un-described sequence type (ST1755: arcc-18, aroe-115, glpf-6, gmk-2 pta-109, tpi-50 and yqil-2; three isolates; 6.67%). Resistance genes proved to be rare. Only three out of 45 isolates (6.67%) carried the beta-lactamase operon. The tetracycline resistance gene tetK was also detected in three isolates (6.67%). Neither the mecA gene, defining MRSA, nor other resistance genes were found. Common virulence markers included leukocidin genes lukD+lukE (in twenty-five isolates; 55.56%), the staphylokinase gene sak (twenty-two isolates; 48.89%), the enterotoxin gene cluster egc (fifteen isolates; 33.33%), and a distinct variant of the enterotoxin A gene (sea-320E, GenBank AY196686.1; thirteen isolates; 28.89%). One CC152 isolate was positive for genes encoding the Panton-Valentine leukocidin (lukF-PV+lukS-PV). This study provides first genotyping data on the population structure and the presence of toxin genes and resistance markers of S. aureus strains in Middle Eastern camels.     

牛源金黄色葡萄球菌凝固酶分型与致病因子检测

为了解青海和甘肃地区奶牛养殖场的金黄色葡萄球菌(S.aureus)基因型分布状况,本研究对来自该两个地区的210份奶样进行了S.aureus的分离与鉴定,利用凝固酶基因(Coa)扩增和限制性内切酶AluⅠ酶切方法对所有分离株进行了凝固酶多态性分型。并对不同凝固酶基因型的S.aureus进行了白细胞毒素F (LukF)、白细胞毒素S (LukS)、α溶血素(α-hemolysin)、β溶血素(β-hemolysin)等主要致病因子检测。结果显示,共分离鉴定出35株S.aureus (青海13株,甘肃22株),所有分离株均能够扩增出Coa基因片段,并有5种PCR分型结果(本文简称PCR1～PCR5型),其中PCR 1、4和5型只有1种亚型,而PCR 2型有3种亚型,PCR 3型有2种亚型。PCR3型是青海(6/13)和甘肃地区(8/22)主要流行的基因型。致病因子检测结果显示,所有分离株均携带致病因子LukS和α溶血素;致病因子LukF和β溶血素检出率也很高,分别是30株(85.7%)和31株(88.6%)。β溶血素基因在甘肃地区检出率为95.5%(21/22),青海地区检出率为76.9%(10/13),致病因子LukF在甘肃地区检出率为91.0%(20/22),青海地区检出率为76.9%(10/13),且在各基因型中均有分布,甘肃地区S.aureus致病因子LukF和β溶血素检出率高于青海地区。本研究首次对青海和甘肃地区致奶牛乳房炎S.aureus进行了鉴定分析,为这两个地区奶牛乳房炎的防治提供了参考依据。     

Staphylococcus aureus: study of genomic similarity of strains isolated in veterinary pathology using amplified fragment length polymorphism (AFLP)

Staphylococcus aureus is a widespread pathogen causing infections in different animal species. The extensive use of antibiotics, particularly methicillin, causes the rise of antibiotic-resistant strains (MRSA). In order to verify the epidemiology and genetic relatedness among MRSA and sensible strains (MSSA), an accurate fingerprinting technique, the amplified fragment length polymorphism (AFLP), was carried out. The isolates were cultured, subdivided on MRSA and MSSA and submitted for the genomic DNA extraction that was utilized for AFLP. The data were analysed for genetic similarity using the Dice coefficient. The results of genomic analysis among MRSA and MSSA and within them revealed that the major component of variation was due to variation within strains (82.12%), while variance among strains was lower (17.88%). The low level of genomic similarity found among S. aureus strains implies high level of genetic diversity. Different similarity was found as well in all strains independently of the source.     

猪链球菌荧光DNA扩增片段长度多态性检测方法的建立

利用荧光标记技术,采用2对引物初步建立检测猪链球菌荧光DNA扩增片段长度多态性方法,结果表明12株猪链球菌扩增的多态性位点数从51～98条不等,该方法能够检测猪链球菌的多态性,区分不同血清型以及同一血清型不同特性的菌株,可用于菌株鉴定及流行病学研究中细菌源的追踪。     

Characterization of methicillin-resistant Staphylococcus aureus CC398 obtained from humans and animals on dairy farms

In this study MRSA isolates from dairy farms were investigated for their genetic relationships and antimicrobial susceptibility. In total, 125 MRSA isolates from 26 dairy farms were studied, including isolates from milk samples (n=46), dairy cattle (n=24), calves (n=6), dust samples from pig (n=16) and veal calf sheds (n=1), dogs (n=2), a horse, a sheep and humans (n=28). CC398-specific PCRs, spa typing, SCCmec typing and ApaI macrorestriction analysis were conducted. Susceptibility testing was performed by broth microdilution. All 125 isolates belonged to CC398. Eight spa types (t011, t108, t034, t567, t1184, t1451, t2287 and t3934) were detected. SCCmec elements of types IV (n=48) and V (n=67) were identified with 10 isolates being non-typeable. Six main macrorestriction patterns - with up to 23 sub-patterns - and twelve resistance patterns were identified. Sixty-eight isolates showed a multiresistance phenotype. Farm-by-farm analysis revealed different scenarios: in some farms, the MRSA CC398 isolates from dairy cattle, humans, pig sheds and/or sheep were indistinguishable suggesting an interspecies exchange of the same MRSA CC398 subtype. In other farms, several MRSA CC398 subtypes were detected in different host species/sources with occasionally even more than one MRSA CC398 subtype from the same host species/source. These latter results may suggest that either different MRSA subtypes associated with humans or animals have been imported into the respective farm or that one MRSA CC398 strain has undergone diversification, reflected by more or less expanded changes in PFGE patterns, spa type or resistance pattern, during colonization of different hosts on the same farm.     

重庆市动物源性金黄色葡萄球菌的分离鉴定及药物敏感性分析

为了解重庆市部分区县动物源性金黄色葡萄球菌的耐药情况,采集重庆市北碚区、合川区、荣昌县部分养殖场466份畜禽粪便样品,将样品划线接种于Mueller-HInton高盐平板,挑取可疑菌落接种LB液体培养基,提取基因组后,通过PCR扩增金黄色葡萄球菌特异性nuc基因,对鉴定的金黄色葡萄球菌进行23种临床常用抗菌药物的药物敏感性试验。结果从466份样品中分离出25株金黄色葡萄球菌,包括17株鸡源菌株和8株猪源菌株。25株临床分离株对23种抗菌药物均有不同程度耐药,对氨苄西林、青霉素G、四环素、强力霉素、林可霉素耐药严重,耐药率超过60%,对阿米卡星、呋喃唑酮、万古霉素只有1株细菌耐药。所有分离菌均为多重耐药。表明分离菌的耐药性严重。本试验结果为重庆市养殖场的临床用药提供了参考,为研究重庆市动物源性金黄色葡萄球菌的耐药基因、耐药机制和耐药传播规律奠定了基础。     

Genotyping of Staphylococcus aureus isolated from various sites on farms with dairy sheep using pulsed-field gel electrophoresis

We investigated the genetic diversity of 179 Staphylococcus aureus isolates recovered from various sites in 10 farms producing cheeses manufactured with raw ewe's milk. Isolates were collected from handcrafted cheeses, bulk tank milk, milk from half-udders, skin abscesses on the udder if present, hands and anterior nares of farmers, and air of the milking area. The isolates were typed using pulsed-field gel electrophoresis (PFGE) of DNA SmaI digests and compared to other isolates of S. aureus isolated in different hosts or in different locations. The results showed that nine farms were contaminated by S. aureus isolates with identical banding patterns (named OV) or by genetically related isolates (named OV'). These dominant banding patterns were found in a variable proportion of the samples from each farm (range: 11-100%). Most of the strains isolated from nasal carriage or strains isolated from other regions or from other animal species had different PFGE patterns to OV or OV', except for three strains. These results show that a single clone of S. aureus is widely distributed both in infected mammary glands and in cheese produced from raw milk. This study confirms that infected mammary glands are the main source of the contamination of dairy products in sheep.     

Distribution of IS900 restriction fragment length polymorphism types among animal Mycobacterium avium subsp. paratuberculosis isolates from Argentina and Europe

Sixty-one Mycobacterium avium subsp. paratuberculosis isolates from cattle and deer from the Buenos Aires province, an important livestock region in Argentina, were typed by restriction fragment length polymorphisms (RFLP) analysis based on IS900. Four different RFLP patterns (designated ‘A’, ‘B’, ‘C’ and ‘E’) were identified in BstEII digests of genomic DNA. The most frequently observed type, pattern ‘A’, was found in 46 isolates (75%). The second, pattern ‘E’, included 8 isolates (13%), while the third, pattern ‘B’, included 6 isolates (10%). Pattern ‘C’ was found for only one isolate. All of the deer isolates were classified as pattern ‘A’, while cattle isolates represented all four RFLP patterns. Twenty-one isolates representing the four different BstEII-RFLP patterns were digested with PstI. Twenty isolates showed identical PstI-RFLP pattern. BstEII-RFLP patterns from Argentine cattle and deer were compared with patterns found in cattle, goat, deer, rabbit, and human isolates from Europe. The most common pattern in Argentina, pattern ‘A’, was identical to a less frequently occurring pattern R9 (C17) from Europe. The other Argentine patterns ‘B’, ‘C’ and ‘E’, were not found in the Europe. These results indicate that the distribution of M. avium subsp. paratuberculosis genotypes in the Buenos Aires province of Argentina is different from that found in Europe.     

Characteristics and epidemiologic genotyping of Staphylococcus aureus isolates from bovine mastitic milk in Hokkaido, Japan

Two hundred thirty one Staphylococcus aureus isolates from bovine mastitic milk were discriminated into 60 patterns and 16 lineages by pulsed-field gel electrophoresis (PFGE). The tested isolates were also investigated using coagulase and capsule serotyping and PCR for possession of genes that encode staphylococcal enterotoxins (sea to sei), enterotoxin-like toxins (selj to selr), and toxic shock syndrome toxin (tst). One hundred seventy three of the isolates (74.9%) possessed one or more toxin genes, while no egg-yolk factor was detected in most of them. The most common combinations of toxin genes possessed by the tested isolates were sec, seg, sei, sell, and tst, or seg and sei, or sec, seg, sei, sell, seln, and tst. Two hundred and ten of the isolates (91.0%) serotyped coagulase VI, and 207 of the isolates (89.6%) expressed serotype 5 or 8 capsules. These results suggested that isolates belonging to two major lineages have spread all over Hokkaido as bovine mastitic isolates. Additionally, no remarkable difference was recognized in the identification ratio of the isolates that belonged to the two major lineages between mastitis of subclinical origin and mastitis of clinical origin.     

Staphylococcus aureus isolates from dairy cows and humans on a farm differ in coagulase genotype

Staphylococcus aureus is a frequent cause of animal and human infections. The aim of the present study was to test diversity of the populations of S. aureus colonising cattle and humans sharing an infected environment. Eighty-six S. aureus isolates obtained from dairy cows, from people coming into contact with dairy cows on the farm and the other farm personnel were characterized by restriction fragment length polymorphism of the coagulase gene. Molecular analyses identified ten polymorphism types with prevalent presentation of type II in isolates from cow's milk and type IV in isolates from people coming into contact with dairy cows on the farm (the cattlemen) and the other farm personnel. Seven further genotypes were identified among the isolates from the cattlemen. The results indicate that the strains dominating in human population did not equate to the causative agents of bovine mastitis.     

Characterization of avian strains of Pasteurella multocida by restriction endonuclease and amplified fragment length polymorphism

Avian strains of Pasteurella multocida were typed by employing restriction endonuclease analysis (REA) and single enzyme-amplified fragment length polymorphism (AFLP) to evaluate their applicability for epidemiological studies of fowl cholera outbreaks. A total of 72 strains isolated from different avian species (chicken, duck, turkey, quail and goose) belonging to various geographical regions of India were characterized. REA using two different enzymes HhaI and HpaII produced 9 and 18 clusters respectively, whereas Single enzyme-AFLP recognized 32 patterns out of 72 strains typed. The study indicated that REA using HpaII is a simple and resource efficient method, however, further typing with more stringent and rapid method like Single enzyme-AFLP, could drastically enhance investigation in epidemiological studies of fowl cholera outbreaks.     

Longitudinal study on the susceptibility to bacteriophages of Staphylococcus aureus strains isolated from dairy farms in Trinidad

A 6-month longitudinal study was conducted on 30 dairy cows in early lactation and their human handlers on six farms across Trinidad. Weekly samples of bulk milk, composite milk and anterior nares and hand swabs from human handlers were collected and cultured for Staphylococcus aureus on Baird-Parker agar (BPA). The susceptibility of S. aureus strains to bacteriophages and the relatedness of strains isolated over the study period were determined. Sixty-three (51.2%) of 123 strains of S. aureus from bulk milk were typable compared with 111 (57.3%) of 194 and 82 (61.7%) of 133 strains isolated from composite milk and human handlers, respectively. The differences were not statistically significant (P > 0.05; chi 2). Bovine phage 42D lysed 3.3% (4 of 123), 16.5% (32 of 194) and 12.0% (16 of 133) of S. aureus strains isolated from bulk milk, composite milk and human handlers, respectively. The differences were statistically significant (P < 0.001; chi 2). Amongst bulk milk isolates of S. aureus, 35 (31.8%) of 110 exhibited relatedness in 11 groups based on their phage patterns and groups. The mean maximum interval between the first and last detection of related S. aureus strains in a group was 11.5 +/- 7.3 weeks. Amongst composite milk strains of S. aureus, 23 (46.0%) of 50, 25 (62.5%) of 40 and 22 (53.7%) of 41 exhibited relatedness on farms IB 2, IB 27 and IC 23, respectively, but the differences were not statistically significant (P > 0.05; chi 2). On farm IB 2, five groups of related strains of S. aureus were detected with a mean maximum interval of detection of 18.2 +/- 8.5 weeks compared to farm IB 27 where five groups of related strains were also observed but with an interval of 13.8 +/- 8.2 weeks. On farm IC 23, a total of seven groups of related S. aureus strains were detected with a mean interval of 8.0 +/- 5.5 weeks. For human strains of S. aureus from farm IB 2, nine (56.3%) of 16 strains isolated from anterior nares exhibited relatedness in three groups with a mean maximum interval of 13.3 +/- 4.7 weeks compared to four (25.0%) of 16 hand swab isolates which exhibited relatedness in two groups with mean interval of detection of 11.0 +/- 1.4 weeks. The differences were not statistically significant (P > 0.05; chi 2). On farm IB 27, for anterior nares isolates, eight (72.7%) of 11 exhibited relatedness in two groups with a mean maximum interval of detection of 20.5 +/- 2.1 weeks compared to hand swab isolates, with six (50.0%) of 12 showing relatedness in two groups and a mean interval of 10.5 +/- 2.1 weeks. It was concluded that dairy cows and their human handlers carried particular strains of S. aureus at various sites for extended periods, which served as continuous sources of contamination of milk and may play a significant role in the occurrence of subclinical mastitis, with an obvious economic impact.     

Differentiation of Mycoplasma gallisepticum strains using amplified fragment length polymorphism and other DNA-based typing methods

Amplified fragment length polymorphism (AFLP) was used to type 34 strains of Mycoplasma gallisepticum (MG) including vaccine strains ts-11, 6/85, and F. Using AFLP, a total of 10 groups, with 30 distinguishable AFLP typing profiles, were generated in the analysis. The AFLP method was able to identify and differentiate both MG field strains from recent outbreaks and those that were epidemiologically related. The AFLP procedure will provide assistance in identifying the sources of mycoplasma infections. Vaccine strains were also differentiated from other field strains, which will be useful in the evaluation of vaccination programs. The AFLP discrimination potential was compared to other molecular typing techniques such as gene-targeted typing by DNA sequence analysis of the MG cytadhesin-like protein encoding gene, mgc2, and random amplified polymorphic DNA assay on the same MG isolates. The three assays correlated well with one another, with AFLP analysis having a much higher discriminatory power and reproducibility.     

Antimicrobial susceptibilities of Staphylococcus aureus isolated from animal and human sources in Brazil

The susceptibilities of 760 Staphylococcus aureus strains isolated from animal infections (400), human infections (300) and healthy human carriers (60) to seven antibiotics were determined by an agar dilution technique. The isolates from human infections were more resistant to a wider spectrum of antibiotics than were the strains from animal infections and healthy human carriers. Amikacin and gentamicin were the most active drugs against all groups of strains.     

Prediction of penicillin resistance in Staphylococcus aureus isolates from dairy cows with mastitis, based on prior test results

AIM: To gauge how well prior laboratory test results predict in vitro penicillin resistance of Staphylococcus aureus isolates from dairy cows with mastitis. METHODS: Population-based data on the farm of origin (n=79), genotype based on pulsed-field gel electrophoresis (PFGE) results, and the penicillin-resistance status of Staph. aureus isolates (n=115) from milk samples collected from dairy cows with mastitis submitted to two diagnostic laboratories over a 6-month period were used. Data were mined stochastically using the all-possible-pairs method, binomial modelling and bootstrap simulation, to test whether prior test results enhance the accuracy of prediction of penicillin resistance on farms. RESULTS: Of all Staph. aureus isolates tested, 38% were penicillin resistant. A significant aggregation of penicillin-resistance status was evident within farms. The probability of random pairs of isolates from the same farm having the same penicillin-resistance status was 76%, compared with 53% for random pairings of samples across all farms. Thus, the resistance status of randomly selected isolates was 1.43 times more likely to correctly predict the status of other isolates from the same farm than the random population pairwise concordance probability (p=0.011). This effect was likely due to the clonal relationship of isolates within farms, as the predictive fraction attributable to prior test results was close to nil when the effect of within-farm clonal infections was withdrawn from the model. CONCLUSIONS: Knowledge of the penicillin-resistance status of a prior Staph. aureus isolate significantly enhanced the predictive capability of other isolates from the same farm. In the time and space frame of this study, clinicians using previous information from a farm would have more accurately predicted the penicillin-resistance status of an isolate than they would by chance alone on farms infected with clonal Staph. aureus isolates, but not on farms infected with highly genetically heterogeneous bacterial strains.     

Genetic differences among Staphylococcus aureus isolates from dairy ruminant species: a single-dye DNA microarray approach

Staphylococcus aureus is recognized worldwide as a major pathogen causing clinical or subclinical intramammary infections in lactating sheep, goats and cows. The present study was carried out to compare 65 S. aureus isolates mainly obtained from nasal carriage and subclinical mastitis in dairy sheep and 43 isolates obtained from subclinical mastitis from 22 goats and 21 cows. A DNA microarray, containing probes against 190 true or putative virulence factors, was used to detect the presence of the virulence genes. Their presence/absence was independently assessed by PCR for the genes of interest. Sheep isolates obtained from the nostrils or the udders did not show any significant tissue specific virulence factor. The dominant pulse-field electrophoresis profile (OV/OV'), associated with spa clonal complex spa-CC 1773, matched mainly with the agr group III and was only found in ovine and caprine isolates. This clone was more specifically characterized by the prevalence of the following virulence genes: lpl4, ssl6, bsaA1, bsaB, bsaP, SAV0812. Moreover, seven virulence-associated genes (lpl1, sel, sec, tst, lukF-PV-like component, lukM, SAV0876) were associated with isolates from small ruminants, while the egc cluster, fhuD1, abiF and SAV2496 with bovine isolates. This genomic study suggests the existence of lineage- and host-specific genes leading to the development of host-specific pathogenic traits of S. aureus isolates.     

Prediction of penicillin resistance in Staphylococcus aureus isolates from dairy cows with mastitis,based on prior test results

AIM: To gauge how well prior laboratory test results predict in vitro penicillin resistance of Staphylococcus aureus isolates from dairy cows with mastitis.

METHODS: Population-based data on the farm of origin (n=79), genotype based on pulsed-field gel electrophoresis (PFGE) results, and the penicillin-resistance status of Staph. aureus isolates (n=115) from milk samples collected from dairy cows with mastitis submitted to two diagnostic laboratories over a 6-month period were used. Data were mined stochastically using the all-possible-pairs method, binomial modelling and bootstrap simulation, to test whether prior test results enhance the accuracy of prediction of penicillin resistance on farms.

RESULTS: Of all Staph. aureus isolates tested, 38% were penicillin resistant. A significant aggregation of penicillin-resistance status was evident within farms. The probability of random pairs of isolates from the same farm having the same penicillin-resistance status was 76%, compared with 53% for random pairings of samples across all farms. Thus, the resistance status of randomly selected isolates was 1.43 times more likely to correctly predict the status of other isolates from the same farm than the random population pairwise concordance probability (p=0.011). This effect was likely due to the clonal relationship of isolates within farms, as the predictive fraction attributable to prior test results was close to nil when the effect of within-farm clonal infections was withdrawn from the model.

CONCLUSIONS: Knowledge of the penicillin-resistance status of a prior Staph. aureus isolate significantly enhanced the predictive capability of other isolates from the same farm. In the time and space frame of this study, clinicians using previous information from a farm would have more accurately predicted the penicillin-resistance status of an isolate than they would by chance alone on farms infected with clonal Staph. aureus isolates, but not on farms infected with highly genetically heterogeneous bacterial strains.     

Distribution of IS900 restriction fragment length polymorphism types among animal Mycobacterium avium subsp. paratuberculosis isolates from Argentina and Europe

Sixty-one Mycobacterium avium subsp. paratuberculosis isolates from cattle and deer from the Buenos Aires province, an important livestock region in Argentina, were typed by restriction fragment length polymorphisms (RFLP) analysis based on IS900. Four different RFLP patterns (designated ‘A’, ‘B’, ‘C’ and ‘E’) were identified in BstEII digests of genomic DNA. The most frequently observed type, pattern ‘A’, was found in 46 isolates (75%). The second, pattern ‘E’, included 8 isolates (13%), while the third, pattern ‘B’, included 6 isolates (10%). Pattern ‘C’ was found for only one isolate. All of the deer isolates were classified as pattern ‘A’, while cattle isolates represented all four RFLP patterns. Twenty-one isolates representing the four different BstEII-RFLP patterns were digested with PstI. Twenty isolates showed identical PstI-RFLP pattern. BstEII-RFLP patterns from Argentine cattle and deer were compared with patterns found in cattle, goat, deer, rabbit, and human isolates from Europe. The most common pattern in Argentina, pattern ‘A’, was identical to a less frequently occurring pattern R9 (C17) from Europe. The other Argentine patterns ‘B’, ‘C’ and ‘E’, were not found in the Europe. These results indicate that the distribution of M. avium subsp. paratuberculosis genotypes in the Buenos Aires province of Argentina is different from that found in Europe.