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Identification of coagulase-negative Staphylococcus species by gas chromatography
Abstract
Researching the impact and epidemiology of coagulase-negative Staphylococcus species (CNS) causing intramammary infections (IMI) require their identification at the species level. Gene sequencing is the gold standard but faster and less expensive methods could be useful. The Sherlock Microbial Identification System is an automated gas chromatographic (MIS-GC) system able to speciate CNS isolates in human clinical medicine by identifying the unique cellular fatty acid patterns in bacteria cell walls. Our objective was to validate the MIS-GC method for speciating CNS responsible for IMI in dairy cows. The CNS isolates examined include 429 isolates of Staphylococcus
chromogenes, 195 Staphylococcus
simulans, 108 Stapylococcus
xylosus, 81 Staphylococcus
haemolyticus and 42 Staphylococcus epidermididis obtained from the Canadian Bovine Mastitis Research Network culture collection and speciated using rpoB gene sequencing. Isolates were harvested from apparently normal mammary quarters before and after the dry period or during lactation. CNS isolates were divided in 2 groups within species. Speciation by MIS-GC of the first group was performed with a human-source CNS fatty-acid profile library and was used to construct a bovine-source library. MIS-GC speciation of the second group was performed with the new library. Repeatability of the technique was evaluated by re-culturing and re-testing a minimum of 50 isolates of each species. Using rpoB sequencing as gold standard, sensitivities for S.
chromogenes, S. simulans, S. xylosus and S. epidermidis with the human library were 63% (n=215), 58% (n=89), 40% (n=55) and 52% (n=21) respectively, and 91%, 79%, 71% and 100% with the bovine library. Repeatability was 80% (n=100), 81% (n=97), 72% (n=53). Sensitivity for S. haemolyticus was 8% with the human library and could not be included in the bovine library. Its repeatability was 90% (n=40). The final bovine library tested on a random sample of S. chromogenes gave a sensitivity of 89%.
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Coagulase-negative staphylococci (CNS) are the most frequently isolated pathogens from cows with intramammary infection (IMI). Although API STAPH ID 20, a commercially available identification system, and PCR-restriction fragment length polymorphism (PCR-RFLP) of the gap gene (gap PCR-RFLP) have been successfully applied for the identification of CNS isolates from human specimens, their accuracy in the identification of veterinary isolates has not been fully established. In this study, we identified 263 CNS isolates from bovine IMI at species level by partial 16S rRNA gene sequence analysis as the definitive test. Species identification obtained using partial 16S rRNA gene sequence analysis was compared to results from the API STAPH ID 20 and gap PCR-RFLP analysis. Eleven different CNS species were identified by partial 16S rRNA gene sequence analysis. Only 76.0% (200/263) of the species identification results obtained by API STAPH ID 20 matched those obtained by partial 16S rRNA gene sequence analysis, whereas 97.0% (255/263) of the species identification results obtained by the gap PCR-RFLP analysis matched those obtained by partial 16S rRNA gene sequence analysis. The gap PCR-RFLP analysis could be a useful and reliable alternative method for the species identification of CNS isolates from bovine IMI and appears to be a more accurate method of species identification than the API STAPH ID 20 system.
Coagulase-negative staphylococci (CNS) have become the most common bovine mastitis isolate in many countries and could therefore be described as emerging mastitis pathogens. The prevalence of CNS mastitis is higher in primiparous cows than in older cows. CNS are not as pathogenic as the other principal mastitis pathogens and infection mostly remains subclinical. However, CNS can cause persistent infections, which result in increased milk somatic cell count (SCC) and decreased milk quality. CNS infection can damage udder tissue and lead to decreased milk production. Staphylococcus simulans and Staphylococcus chromogenes are currently the predominant CNS species in bovine mastitis. S. chromogenes is the major CNS species affecting nulliparous and primiparous cows whereas S. simulans has been isolated more frequently from older cows. Multiparous cows generally become infected with CNS during later lactation whereas primiparous cows develop infection before or shortly after calving. CNS mastitis is not a therapeutic problem as cure rates after antimicrobial treatment are usually high. Based on current knowledge, it is difficult to determine whether CNS species behave as contagious or environmental pathogens. Control measures against contagious mastitis pathogens, such as post-milking teat disinfection, reduce CNS infections in the herd. Phenotypic methods for identification of CNS are not sufficiently reliable, and molecular methods may soon replace them. Knowledge of the CNS species involved in bovine mastitis is limited. The dairy industry would benefit from more research on the epidemiology of CNS mastitis and more reliable methods for species identification.
The lack of an adequate typing system hampers our understanding of the epidemiology of infections caused by coagulase-negative staphylococci (CoNS). CoNS have become recognized as important nosocomial pathogens and the principal cause of infections associated with invasive devices. Sensitive, specific, and convenient methods are needed to evaluate whether implementing infection control guidelines reduces the risk of nosocomial infections from CoNS and other pathogens. The Microbial Identification System (MIDI) (Microbial ID Inc., Newark, Del.), a semiautomated system for fatty acid methyl ester analysis, shows considerable promise for clinical and epidemiologic applications. Its predictive accuracy and reliability were tested by using epidemiologically related and replicated CoNS isolates as well as CoNS from epidemiologically unrelated clinical infections, which were obtained from five established hospital culture collections in diverse geographic locations. Two hundred isolates were fully characterized in 5 days by one person using MIDI, and the results were similar to those produced by more expensive and time-consuming conventional typing methods. MIDI appears to be a useful screening tool that could be used before more expensive and labor-intensive molecular methods. It offers important advantages to hospital epidemiologists and clinical microbiologists who must identify and type CoNS isolates.
A survey of clinical and subclinical mastitis was carried out on 97 dairy farms in England and Wales, selected at random from members of a national milk recording scheme. The farmers were asked to collect aseptic milk samples from five consecutive cases of clinical mastitis and from five quarters with high somatic cell counts using a defined protocol, and they completed a questionnaire that included information on the cows sampled, the herd and the history of mastitis in the herd. The samples were collected throughout the year. The mean incidence of clinical mastitis was 47 cases per 100 cows per year (estimated from historic farm records) and 71 cases per 100 cows per year (estimated from the samples collected). Streptococcus uberis and Escherichia coli were isolated in pure culture from 23.5 per cent and 19.8 per cent, respectively, of the clinical samples; 26.5 per cent of the clinical samples produced no growth. The most common isolates from the samples with high cell counts were coagulase-negative staphylococci (15 per cent), S uberis (14 per cent) and Corynebacterium species (10 per cent). Staphylococcus aureus and coagulase-positive staphylococci together accounted for 10 per cent of the samples with high somatic cell counts; 39 per cent produced no bacterial growth.
Costs and feasibility of extensive sample collection and processing are major obstacles to mastitis epidemiology research. Studies are often consequentially limited, and fundamental mastitis researchers rarely have the opportunity to conduct their work in epidemiologically valid populations. To mitigate these limitations, the Canadian Bovine Mastitis Research Network has optimized research funds by creating a data collection platform to provide epidemiologically meaningful data for several simultaneous research endeavors. This platform consists of a National Cohort of Dairy Farms (NCDF), Mastitis Laboratory Network, and Mastitis Pathogen Culture Collection. This paper describes the implementation and operation of the NCDF, explains its sampling protocols and data collection, and documents characteristics, strengths and limitations of these data for current and potential users. The NCDF comprises 91 commercial dairy farms in 6 provinces sampled over a 2-yr period. Primarily Holstein-Friesian herds participating in Dairy Herd Improvement milk recording were selected in order to achieve a uniform distribution among 3 strata of bulk tank somatic cell counts and to reflect regional proportions of freestall housing systems. Standardized protocols were implemented for repeated milk samplings on clinical mastitis cases, fresh and randomly selected lactating cows, and cows at dry-off and after calving. Just fewer than 133,000 milk samples were collected. Demographic and production data were recorded at individual cow and farm levels. Health management data are documented and extensive questionnaire data detailing farm management and cleanliness information are also captured. The Laboratory Network represents coordinated regional mastitis bacteriology laboratories using standardized procedures. The Culture Collection archives isolates recovered from intramammary infections of cows in the NCDF and contains over 16,500 isolates, all epidemiologically cross-referenced between linked databases. The NCDF is similar to Canadian dairies in relation to mean herd size, average production, and freestall percentages. Pathogen recovery was greater than anticipated, particularly for coagulase-negative staphylococci and Corynebacterium spp. International scientists are encouraged to use this extensive archive of data and material to enhance their own mastitis research.
A survey was carried out in 2003 in 49 dairy herds to determine the overall and pathogen-specific prevalence of intramammary infection (IMI) in Dutch dairy herds, and to compare the distribution with four studies performed from 1973 to 1985 in The Netherlands. Herds were randomly selected stratified over the 12 Dutch provinces, had at least 40 lactating cows and participated in the Dutch milk recording system. Quarter milk samples were collected from all 408 cows with a somatic cell count (SCC) >or=250,000 cells/ml and 145 heifers with SCC >or=150,000 cells/ml at the last milk test before the farm visit. Additionally, samples were collected from 519 (approximately 25%) of the remaining low-SCC cows and heifers with a SCC at the last milk test before the farm visit of <250 000 and <150 000 cells/ml, respectively. Bacterial growth occurred in 37.3% of milk samples of high-SCC cows and in 21.1% of low-SCC cows. Coagulase-negative staphylococci (CNS) were the most frequently isolated group of bacteria (10.8% of quarters) and were found in all herds. Prevalence of Staphylococcus aureus IMI was lower in 2003 than in 1973, respectively 1.8% and 6.2% of quarters. Prevalence of Streptococcus uberis and Str. dysgalactiae IMI was almost the same in the five samplings during the 30-year period, at 1.1-1.7 and 0.9-1.5%, respectively. Str. agalactiae was not found in this study. Prevalence of CNS IMI was higher in lactating heifers, while prevalence of Str. uberis, Str. dysgalactiae and penicillin-resistant Staph. aureus IMI was higher in older cows. Because distribution of pathogens changes over time, herd-level samples for bacteriological culturing must be taken regularly to monitor udder health. Additionally, national mastitis prevalence studies give important information through monitoring the national udder health status.
In this study, the accuracy of two phenotypic tests, API Staph ID 32 and Staph-Zym, was determined for identification of coagulase-negative staphylococci (CNS) from bovine milk samples in comparison with identification based on DNA-sequencing. A total of 172 CNS isolated from bovine milk were classified into 17 species. The most frequently isolated species based on rpoB sequencing were Staphylococcus chromogenes and Staphylococcus epidermidis, followed by Staphylococcus xylosus, Staphylococcus warneri and Staphylococcus equorum (37, 13, 9, 8 and 6% of isolates, respectively). The API Staph ID 32 correctly identified 41% of the CNS isolates. Best agreement with rpoB sequence based species identification was found for S. epidermidis, Staphylococcus hyicus and S. xylosus (100, 89 and 87%, respectively). The positive predictive value was 89, 100 and 52%, respectively. Poor sensitivity was observed for 3 of the 5 most frequently found species, S. chromogenes (37%), Staphylococcus warneri (15%) and S. equorum (0%) albeit with specificity of 100%. The Staph-Zym needed additional tests for 66% of the isolates and identified 31% of the CNS isolates correctly. Good sensitivity was found for S. epidermidis, S. simulans and S. xyloxus (100, 78 and 73%, respectively). The positive predictive value was 89, 78 and 98%, respectively. Poor sensitivity was observed for S. chromogenes, S. warneri and S. equorum (0, 54 and 0%, respectively) but with a specificity of 100, 99 and 100%, respectively. Both phenotypic tests misidentified a large proportion of CNS isolates and were thus unsuitable for identification of CNS species from bovine milk samples.
Coagulase-negative staphylococci (CNS) are isolated commonly from bovine milk and skin. Their impact on udder health and milk quality is debated. It has been suggested that sources and consequences of infection may differ between CNS species. Species-specific knowledge of the impact and epidemiology of CNS intramammary infections is necessary to evaluate whether species-specific infection control measures are feasible and economically justified. Accurate measurement of impact, sources, and transmission mechanisms requires accurate species level identification of CNS. Several phenotypic and genotypic methods for identification of CNS species are available. Many methods were developed for use in human medicine, and their ability to identify bovine CNS isolates varies. Typeability and accuracy of typing methods are affected by the distribution of CNS species and strains in different host species, and by the ability of test systems to incorporate information on new CNS species into their experimental design and reference database. Generally, typeability and accuracy of bovine CNS identification are higher for genotypic methods than for phenotypic methods. As reviewed in this paper, DNA sequence-based species identification of CNS is currently the most accurate species identification method available because it has the largest reference database, and because a universally meaningful quantitative measure of homology with known species is determined. Once sources, transmission mechanisms, and impact of different CNS species on cow health, productivity and milk quality have been identified through use of epidemiological data and accurate species identification methods, appropriate methods for routine use in research and diagnostic laboratories can be proposed.
In order to evaluate the usefulness of some phenotypic and genotypic methods for species identification of coagulase-negative staphylococci (CNS), isolates were obtained from bovine cases of clinical and sub-clinical mastitis from different geographical areas in Sweden. By using the Staph-Zym test, antimicrobial susceptibility testing, and sequencing of part of the CNS tuf gene and, when needed, part of the 16S rRNA gene we characterized 82 clinical isolates and 24 reference strains of 18 different species of staphylococci. The genotypic methods identified nine different species of CNS among the 82 milk isolates. A comparison with results obtained by tuf gene sequencing showed that Staph-Zym correctly identified CNS reference strains to species level more often than bovine milk CNS isolates (83% and 61%, respectively). In addition, tests supplementary to the Staph-Zym were frequently needed in both groups of isolates (50% of reference strains and 33% of milk isolates) to obtain an identification of the strain. It is notable that Staph-Zym judged two isolates as CNS, although they belonged to other species, could not give a species name in 11% of the bovine CNS isolates, and gave 28% of the isolates an incorrect species name. The present study indicates that the studied phenotypic methods are unreliable for identification of CNS from bovine intra-mammary infections.
The complete sequence of rpoB, the gene encoding the beta subunit of RNA polymerase was determined for Staphylococcus saccharolyticus, Staphylococcus lugdunensis, S taphylococcus caprae, and Staphylococcus intermedius and partial sequences were obtained for an additional 27 Staphylococcus species. The complete rpoB sequences varied in length from 3,452 to 3,845 bp and had a 36.8 to 39.2% GC content. The partial sequences had 71.6 to 93.6%
interspecies homology and exhibited a 0.08 to 0.8% intraspecific divergence. With a few exceptions, the phylogenetic relationships
inferred from the partial rpoB sequences were in agreement with those previously derived from DNA-DNA hybridization studies and analyses of 16S ribosomal
DNA gene sequences and partial HSP60 gene sequences. The staphylococcal rpoB sequence database we established enabled us to develop a molecular method for identifying Staphylococcus isolates by PCR followed by direct sequencing of the 751-bp amplicon. In blind tests, this method correctly identified 10
Staphylococcus isolates, and no positive results were obtained with 10 non-Staphylococcus gram-positive and gram-negative bacterial isolates. We propose partial sequencing of the rpoB gene as a new tool for the accurate identification of Staphylococcus isolates.
The main objective was to determine the prevalence of intramammary infections (IMI) in dairy cows in Flanders, Belgium. Data were obtained from quarter milk samples of dairy herds subjected to a mandatory yearly screening of all lactating cows. A total of 178,668 quarter milk samples were collected at 1087 cross-sectional dairy herd screenings performed in three consecutive years. Of the dairy cows, 40% had at least one culture-positive quarter. More than 50% of all IMI were caused by non-aureus staphylococci. Streptococcus agalactiae is almost eradicated in Flanders, whereas Staphylococcus aureus was isolated from 18% of the culture-positive quarters. In addition, the distribution of mastitis pathogens in quarter milk samples from selected dairy cows with an elevated somatic cell count (SCC) is described. From 6390 cows with a geometric mean composite SCC 250,000 cells/ml, nearly 65% had at least one culture-positive quarter. The majority of the IMI were caused by non-aureus staphylococci (41.1%), whereas Staph. aureus and aesculin-positive cocci were found in respectively 25% and 18% of the culture-positive milk samples. We conclude that more efforts are needed in the prevention and control of subclinical mastitis in Flanders. Non-aureus staphylococci are the predominant cause of IMI, warranting more research regarding the epidemiology and pathogenicity of those species.