Short communication: Identification of subclinical cow mastitis pathogens in milk by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Subclinical mastitis is a common and easily disseminated disease in dairy herds. Its routine diagnosis via bacterial culture and biochemical identification is a difficult and time-consuming process. In this work, we show that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) allows bacterial identification with high confidence and speed (1 d for bacterial growth and analysis). With the use of MALDI-TOF MS, 33 bacterial culture isolates from milk of different dairy cows from several farms were analyzed, and the results were compared with those obtained by classical biochemical methods. This proof-of-concept case demonstrates the reliability of MALDI-TOF MS bacterial identification, and its increased selectivity as illustrated by the additional identification of coagulase-negative Staphylococcus species and mixed bacterial cultures. Matrix-assisted laser desorption-ionization mass spectrometry considerably accelerates the diagnosis of mastitis pathogens, especially in cases of subclinical mastitis. More immediate and efficient animal management strategies for mastitis and milk quality control in the dairy industry can therefore be applied.     

16S rRNA基因序列、生化鉴定、质谱3类方法鉴定常见微生物的结果分析

目的比较16SrRNA基因序列、生化鉴定、质谱鉴定3类实验方法分析沙门氏菌、金黄色葡萄球菌、蜡样芽孢杆菌的鉴定结果的异同。方法挑选沙门氏菌、金黄色葡萄球菌、蜡样芽孢杆菌各50株,分别进行16S rRNA基因序列测定、VITEK COMPACT 2生化鉴定、质谱鉴定3类实验,并比较3类实验的鉴定结果。结果 3类实验方法对大部分沙门氏菌鉴定在属水平,生化鉴定方法对少数血清型鉴定到种水平;对金黄色葡萄球菌均鉴定到种水平; 16SrRNA基因序列、生化方法对蜡样芽孢杆菌鉴定到属水平,质谱鉴定到种水平。结论 3类实验方法对大部分沙门氏菌、所有金黄色葡萄球菌鉴定水平相同,质谱鉴定蜡样芽孢杆菌的结果更准确,且质谱鉴定时效性更高。     

Isolation and characterization of Streptococcus parauberis from vacuum-packaging refrigerated seafood products

Streptococcus parauberis is known as an etiological agent of mastitis in cows and for producing streptococcosis in farmed fish, although its presence in foods has seldom been reported. In this work, two bacterial isolates were recovered from a spoiled vacuum-packaged refrigerated seafood product. Both isolates were identified by 16S rRNA gene sequencing, exhibiting 99% homology with respect to S. parauberis. Both isolates were also characterized by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Genetic analysis revealed the clonal homogeneity of the isolates and their grouping together with other S. parauberis strains in a different cluster with respect to Streptococcus uberis strains. Proteomic analysis by MALDI-TOF MS allowed for the identification of five mass peaks in the range of 2200–6000 m/z that resulted to be specific to the species S. parauberis and allowed its rapid and direct identification with respect to other pathogenic and spoilage bacteria potentially present in seafood and other food products. This study represents, to our knowledge, the first report of S. parauberis in seafood in general and in vacuum-packed food products in particular. Moreover, it provides a rapid method based on MALDI-TOF MS for the identification of S. parauberis.     

Short communication: Genotypic and phenotypic identification of environmental streptococci and association of Lactococcus lactis ssp. lactis with intramammary infections among different dairy farms

Lactococcus species are counted among a large and closely related group of environmental streptococci and streptococci-like bacteria that include bovine mastitis pathogenic Streptococcus, Enterococcus, and Aerococcus species. Phenotypic and biochemical identification methods can be inaccurate and unreliable for species within this group, particularly for Lactococcus spp. As a result, the incidence of Lactococcus spp. on the farm may have been historically underreported and consequently little is known about the clinical importance of this genus as a mastitis pathogen. We used molecular genetic identification methods to accurately differentiate 60 environmental streptococci and streptococci-like bacteria isolated from cows with high somatic cell count and chronic intramammary infection (IMI; >2 somatic cell scores above 4) among 5 geographically distinct farms in New York and Minnesota that exhibited an observed increase in IMI. These isolates were phenotypically identified as Streptococcus uberis and Streptococcus spp. Genetic methods identified 42 isolates (70%) as Lactococcus lactis ssp. lactis, including all 10 isolates originally phenotypically identified as Streptococcus uberis. Antibiotic inhibition testing of all Lc. lactis ssp. lactis showed that 7 isolates were resistant to tetracycline. In the present study, a predominance of Lc. lactis ssp. lactis was identified in association with chronic, clinical bovine IMI among all 5 farms and characterized antimicrobial resistance for treatment therapies. Routine use by mastitis testing labs of molecular identification methods for environmental streptococci and streptococci-like bacteria can further define the role and prevalence of Lc. lactis ssp. lactis in association with bovine IMI and may lead to more targeted therapies.     

Matrix-assisted laser desorption and ionization-time-of-flight mass spectrometry, 16S rRNA gene sequencing, and API 32E for identification of Cronobacter spp.: a comparative study

Twenty-two isolates of the family Enterobacteriaceae, with focus on Cronobacter isolated from infant formula and the environment of milk powder plants, were comparatively identified using API 32E (bioMérieux, Marcy l'Etoile, France), 16S rRNA gene sequencing (Accugenix, Newark, USA), and matrix-assisted laser desorption and ionization-time-of-flight mass spectrometry (MALDI-TOF MS; Mabritec, Riehen, Switzerland and AnagnosTec, Potsdam, Germany). With API 32E, 22% of the isolates were assigned to species, 64% were assigned to a genus, and 14% could not be discriminated at any taxonomic level. Both 16S rRNA gene sequencing and MALDI-TOF MS assigned 100% of the isolates to species, but the identifications based on MALDI-TOF MS results were more discriminating and unequivocal. Our data indicate that MALDI-TOF MS provides the most rapid and unambiguous identification of Cronobacter and closely related Enterobacteriaceae isolates.     

Identification and differentiation of brewery isolates of Pectinatus sp. by Matrix-Assisted-Laser Desorption–Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)

Members of the genus Pectinatus (P.) are feared contaminants in the brewing industry as their growth in beer results in the production of metabolites, which cause serious off-flavors such as hydrogen sulfide. Thus, identification and differentiation of the species P. cerevisiiphilus, P. frisingensis and P. haikarae is of vital interest. Nineteen isolates of Pectinatus were analyzed by matrix-assisted-laser desorption–ionization time-of-flight mass spectrometry (MALDI-TOF MS). Reference spectra were recorded for four isolates representing the three species P. cerevisiiphilus, P. frisingensis and P. haikarae, which enabled reliable identification of the remaining fifteen isolates as P. frisingensis. All isolates were further examined to investigate MALDI-TOF MS’s potential to differentiate between various isolates of Pectinatus species. Upon generation of reference database spectra, sixteen out of nineteen isolates could be distinguished based on differences in their MALDI-TOF MS fingerprint. Two out of three misidentifications occurred between highly similar isolates originating from the same brewery. As MALDI-TOF MS spectra were reliably assigned to the corresponding isolate in more than 80 % of all cases, the application of MALDI-TOF MS could help to track contaminants in the production system and to monitor efforts to eliminate them.     

基质辅助激光解吸电离飞行时间质谱与VITEK和rpoB基因测序三种方法对食品中葡萄球菌鉴定效果的比较

目的 比较基质辅助激光解吸电离飞行时间质谱(matrix-assisted laser desorption/ionization time-of-flight mass spectrometry,MALDI-TOF MS)、rpoB基因测序和VITEK 2 Compact三种方法对葡萄球菌的鉴定效果。方法 同时采用三种方法对实验室保存的从食品中分离的59株葡萄球菌进行鉴定。结果 MALDI-TOF MS法和rpoB基因测序法一致性达100.00%,与VITEK 2 Compact法的一致性为83.05%(49/59)。7株菌因超出VITEK 2 Compact鉴定范围而鉴定错误。MALDI-TOF MS法可快速将59株菌准确鉴定为17种葡萄球菌,鉴定分值与细菌种类相关。金黄色葡萄球菌的鉴定分值最高(>2.300),松鼠葡萄球菌、鱼发酵葡萄球菌和琥珀葡萄球菌的鉴定分值相对较低(1.700～2.000)。结论 相比rpoB基因测序法和VITEK 2 Compact法,MALDI-TOF MS法更加快速准确。为达到更好的鉴定效果,现有数据库仍需进一步优化。     

Short communication: Evaluation of MALDI-TOF mass spectrometry and a custom reference spectra expanded database for the identification of bovine-associated coagulase-negative staphylococci

This study evaluated MALDI-TOF mass spectrometry and a custom reference spectra expanded database for the identification of bovine-associated coagulase-negative staphylococci (CNS). A total of 861 CNS isolates were used in the study, covering 21 different CNS species. The majority of the isolates were previously identified by rpoB gene sequencing (n = 804) and the remainder were identified by sequencing of hsp60 (n = 56) and tuf (n = 1). The genotypic identification was considered the gold standard identification. Using a direct transfer protocol and the existing commercial database, MALDI-TOF mass spectrometry showed a typeability of 96.5% (831/861) and an accuracy of 99.2% (824/831). Using a custom reference spectra expanded database, which included an additional 13 in-house created reference spectra, isolates were identified by MALDI-TOF mass spectrometry with 99.2% (854/861) typeability and 99.4% (849/854) accuracy. Overall, MALDI-TOF mass spectrometry using the direct transfer method was shown to be a highly reliable tool for the identification of bovine-associated CNS.     

Short communication: Lack of intramammary niche recolonization during a sanitation program for the contagious mastitis pathogen Staphylococcus aureus genotype B

In Switzerland, sanitation programs of dairy herds infected with the contagious mastitis pathogen Staphylococcus aureus genotype B (GTB) have been established for several years. In recent years, Streptococcus uberis and non-aureus staphylococci have emerged as the bacteria most frequently isolated from bovine milk samples. The latter cause subclinical mastitis, and some species are more persistent or pathogenic than others. The present study aimed to investigate the developments in the intramammary colonization spectrum of 5 dairy herds undergoing a sanitation program for Staph. aureus GTB. We collected single-quarter milk samples aseptically from all lactating cows at 3-mo intervals during the sanitation period; after classical bacteriological analysis, MALDI-TOF mass spectrometry was used to identify the isolates to the species level. Non-aureus staphylococci were found to be the bacterial group most frequently occurring on the selected farms, with Staphylococcus chromogenes and Staphylococcus xylosus being predominant. The present study demonstrated that GTB-infected cows treated with antibiotics lacked systematic recolonization with other bacteria during herd sanitation for the contagious Staph. aureus GTB.     

Evaluation of simplified and commercial systems for identification of foodborne yeasts

Commercial identification kits (API 20C, API Yeast-Ident and API-Zym) were compared with a conventional but simplified identification method (SIM) for identifying seventy-two yeast isolates from fresh sweet corn. SIM failed to provide identification of two isolates. Of the twenty species identified, only eleven were included in the API 20C profile index. Three isolates were identified at the species level and three were identified at the genus level with 100% accuracy. The enzyme kit (Yeast-Ident) gave rather unreliable results, in that identification of only four isolates with 75 to 85% of appropriate reactions was made. The API 20C kit could be used to identify non-clinical yeasts, provided they were included in its database and a few additional tests (urease reaction, nitrate assimilation and glucose fermentation) were also performed.     

金黄色葡萄球菌基质辅助激光解析电离-飞行时间质谱的鉴定与聚类分型

目的 建立基质辅助激光解吸电离-飞行时间质谱法(matrix assisted laser desorption lonization-time of flight mass spectrometer, MALDI-TOF MS)快速鉴定金黄色葡萄球菌(Staphylococcus aureus, S. aureus)并自建数据库, 进行聚类分型。方法 基于MALDI-TOF MS技术, 对经全自动微生物分析仪(VITEK2 COMPACT)鉴定为S. aureus的25株分离株和1株标准菌株(ATCC 25923)进行鉴定。并进一步采集26株S. aureus特征性蛋白质指纹图谱, 使用flex Analysis软件进行分析, 汇总成标准图谱并构建本地分离株S. aureus的鉴定数据库, 命名为Staphylococcus aureus。结果 经标准菌株ATCC 25923验证, 自建数据库对S. aureus鉴定结果的可信度较设备自带数据库明显提高, 鉴定分值由2.251提高到了2.845。自建数据库进一步对26株S. aureus进行聚类分型, 在差异水平100时, 24株不同来源S. aureus被聚类成24个分支, 将食品中不同来源分离的S. aureus分为24个型。结论 MALDI-TOF MS作为一种快速、准确、高通量的全新微生物鉴定技术, 实现了对S. aureus的特异性快速鉴定与分型, 能够满足公共安全卫生、突发食品安全事件和口岸快速通关方面的需求。     

基质辅助激光解吸电离飞行时间质谱法对环境中芽孢杆菌的鉴定及溯源

目的 使用基质辅助激光解吸电离飞行时间质谱技术 (matrix assisted laser desorption lionization-time of flight mass spectrometer, MALDI-TOF MS)，对芽孢杆菌进行快速鉴定和聚类分析，用于研究MALDI-TOF MS对芽孢杆菌溯源的可行性。方法 对实验菌株纯化培养后，使用甲酸提取法提取实验菌株蛋白，并使用MALDI-TOF MS，对22株环境分离菌株和1株标准菌株(CGMCC(B)1.1086)进行鉴定。进一步采集22株实验菌株的蛋白质指纹图谱，使用SARAMIS软件，对实验菌株进行聚类分析。结果 经鉴定，标准菌株(CGMCC(B)1.1086)的鉴定结果可信度为99.9%。22株环境菌均为芽孢杆菌，其中，6株菌鉴定到属水平，16株菌鉴定到种水平。在相似水平为80%的条件下，22株芽孢杆菌分为22个分支。结论 可以使用MALDI-TOF MS对芽孢杆菌进行快速鉴定与分型，对于微生物溯源有重要意义，能够满足食品检测及溯源的需求。     

Coagulase-negative staphylococci isolated from bovine extramammary sites and intramammary infections in a single dairy herd

Isolates of various species of coagulase-negative staphylococci (CNS) from extramammary swab samples were compared with isolates of bovine mastitis CNS species. Swab samples were taken from perineum skin and udder skin, teat apices and teat canals of lactating dairy cows of the research dairy herd of the University of Helsinki in 1999 and 2002. In addition, hands of herd staff and liners of teat cups were sampled for CNS. CNS isolates from milk samples of subclinical or clinical mastitis in the same herd were collected during 1998-2002. Species identification was performed using phenotyping (API Staph ID 32 test) and by constructing a 16 and 23S rRNA RFLP library (ribotyping). Based on phenotype, 84% of mastitis isolates and 57% of extramammary isolates were identified at species level with >90% probability. Ribotype patterns formed 24 clusters, and 15 of them included a CNS type strain. If the ribotype clusters contained isolates of both extramammary and mastitis origin, they were further typed using pulsed-field gel electrophoresis (PFGE). The predominant CNS species in mastitis, based both on phenotyping and genotyping, were Staph. chromogenes and Staph. simulans. Phenotyping failed to identify half of the extramammary isolates. Based on phenotyping, Staph. equorum and Staph. sciuri, and based on ribotyping, Staph. succinus and Staph. xylosus, were the predominant CNS species in extramammary samples. The most common species in milk samples, Staph. chromogenes, was also isolated from several extramammary samples, and five out of ten pulsotypes were shared between mastitis and extramammary isolates, indicating that strains from udder skin are highly similar. The second commonest mastitis species, Staph. simulans, was isolated only from three extramammary samples, indicating that Staph. simulans may be more specifically associated with mastitis. Consequently, the origin of CNS mastitis may vary depending on the causing CNS species.     

Identification of bovine-associated coagulase-negative staphylococci by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry using a direct transfer protocol

This study evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) for the identification of bovine-associated coagulase-negative staphylococci (CNS), a heterogeneous group of different species. Additionally, we aimed to expand the MALDI-ToF MS database with new reference spectra as required to fill the gaps within the existing commercial spectral library. A total of 258 isolates of CNS were used in the study, covering 16 different CNS species. The majority of the isolates were previously identified by rpoB gene sequencing (n = 219), and the remainder were identified by sequencing of 16S rRNA, hsp60, or both rpoB and hsp60. The genotypic identification was considered the gold standard identification. All MALDI-ToF MS identifications were carried out using the direct transfer method. In a preliminary evaluation (n = 32 isolates; 2 of each species) with the existing commercial database, MALDI-ToF MS showed a typeability of 81% (26/32) and an accuracy of 96% (25/26). In the main evaluation (n = 226 isolates), MALDI-ToF MS with the existing commercial Biotyper (Bruker Daltonics Inc., Billerica, MA) database achieved a typeability of 92.0% (208/226) and an accuracy of 99.5% (207/208). Based on the assessment of the existing commercial database and prior knowledge of the species, a total of 13 custom reference spectra, covering 8 species, were created and added to the commercial database. Using the custom reference spectra expanded database, isolates were identified by MALDI-ToF MS with 100% typeability and 100% accuracy. Whereas the MALDI-ToF MS manufacturer's cutoff for species-level identification is 2.000, the reduction of the species level cutpoint to ≥1.700 improved the species-level identification rates (from 64 to 92% for the existing commercial database) when classifying CNS isolates. Overall, MALDI-ToF MS using the direct transfer method was shown to be a highly reliable tool for the identification of bovine-associated CNS.     

Potential and limitations of MALDI-TOF MS for discrimination within the species Leuconostoc mesenteroides and Leuconostoc pseudomesenteroides

The discriminatory power of MALDI-TOF MS (matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry) was evaluated for differentiation of bacterial strains within Leuconostoc mesenteroides and Leuconostoc pseudomesenteroides species. Protein fingerprints were generated with MALDI-TOF MS for 24 Leuconostoc strains and analyzed with ClinProTools at species level and below. A treatment of bacterial cells prior to MALDI-TOF MS analysis was optimized applying different lysozyme concentrations. A pre-treatment with a lysozyme concentration of 12.5 μg ml^?1 for 30 min exposure time enhanced the reproducibility of the spectra but did not influence the cluster analysis in ClinProTools. The cluster analysis resulted in the identification of seven different peak patterns shared among twelve strains of L. pseudomesenteroides and eight peak patterns shared among twelve strains of L. mesenteroides. The protein fingerprints of 24 Leuconostoc strains were sufficiently diverse for a reliable discrimination of half of the analyzed starter cultures at strain level. The other half of the strains could only be identified at cluster level. The discrimination at subspecies level was not possible on the basis of MALDI-TOF MS profiling. The MALDI-TOF MS methodology delivered interesting information about the diversity of bacterial isolates belonging to the two species L. mesenteroides and L. pseudomesenteroides but had its limitations for subspecies discrimination of unknown isolates as well as strain identification.     

Assessment of the main pathogens associated with clinical and subclinical endometritis in cows by culture and MALDI-TOF mass spectrometry identification

Clinical endometritis (CE) and subclinical endometritis (SCE) are diseases that affect dairy cows during the puerperium, causing negative effects on the animals' milk production and fertility. The objective of this study was to assess the main bacteria related to cases of CE and SCE from uterine samples of dairy cows in Brazilian herds. Selective and differential media were used for isolation of aerobic and anaerobic bacteria and further MALDI-TOF mass spectrometry (MS) identification. A total of 279 lactating dairy cows with 28 to 33 d in milk from 6 commercial farms were evaluated. Initially, cows were classified in 3 groups: cytologic healthy cows (n = 161), cows with CE (n = 83), and cows with SCE (n = 35). Healthy animals presented 97 species, followed by the CE group with 53 identified species, and SCE cows presented only 21 bacterial species. We found a significantly higher isolation rate of Trueperella pyogenes in CE (26.5%) cows compared with healthy and SCE cows. Some anaerobic species were exclusively isolated from the CE group, even though they presented lower frequency. Interestingly, 18.1% of samples from CE cows and 40% of SCE cows were negative to bacterial isolation. Despite the use of culture-dependent methods instead of molecular methods, the present study enabled the identification of a complex community of 127 different species from 48 genera, composed of aerobic and anaerobic bacterial species among the 3 different animal groups. The method of sample collection, culture, and identification by MALDI-TOF MS were essential for the success of the analyses.     

Rapid and accurate bacterial identification in probiotics and yoghurts by MALDI-TOF mass spectrometry

Probiotic food is manufactured by adding probiotic strains simultaneously with starter cultures in fermentation tanks. Here, we investigate the accuracy and feasibility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for bacterial identification at the species level in probiotic food and yoghurts. Probiotic food and yoghurts were cultured in Columbia and Lactobacillus specific agar and tested by quantitative real-time PCR (qPCR) for the detection and quantification of Lactobacillus sp. Bacterial identification was performed by MALDI-TOF analysis and by amplification and sequencing of tuf and 16S rDNA genes. We tested 13 probiotic food and yoghurts and we identified by qPCR that they presented 10(6) to 10(7) copies of Lactobacillus spp. DNA/g. All products contained very large numbers of living bacteria varying from 10(6) to 10(9) colony forming units/g. These bacteria were identified as Lactobacillus casei, Lactococcus lactis, Bifidobacterium animalis, Lactobacillus delbrueckii, and Streptococcus thermophilus. MALDI-TOF MS presented 92% specificity compared to the molecular assays. In one product we found L. lactis, instead of Bifidus spp. which was mentioned on the label and for another L. delbrueckii and S. thermophilus instead of Bifidus spp. MALDI-TOF MS allows a rapid and accurate bacterial identification at the species level in probiotic food and yoghurts. Although the safety and functionality of probiotics are species and strain dependent, we found a discrepancy between the bacterial strain announced on the label and the strain identified. Practical Application: MALDI-TOF MS is rapid and specific for the identification of bacteria in probiotic food and yoghurts. Although the safety and functionality of probiotics are species and strain dependent, we found a discrepancy between the bacterial strain announced on the label and the strain identified.     

克罗诺杆菌属食品分离株种水平鉴定方法比较研究

目的研究食品中分离克罗诺杆菌属种的鉴定方法,旨在建立稳定、可靠的种的鉴定方法。方法本研究选择三种鉴定方法,包括生化鉴定(VITEK 2 Compact)法、基质辅助激光解吸电离飞行时间质谱(MALDI-TOF MS)、全基因组测序,通过比较分析三种方法对19株克罗诺杆菌属的鉴定结果,阐述三种鉴定方法的优缺点及其适用性。结果本研究中19株克罗诺杆菌属的鉴定结果显示,VITEK 2 Compact对阪崎克罗诺杆菌和丙二酸盐克罗诺杆菌的鉴定准确率只有67%和66%,而MALDI-TOF MS和全基因组测序的鉴定结果一致,因此可以判定MALDI-TOF MS能够快速、准确、高通量对克罗诺杆菌属进行种的鉴定。但是MALDI-TOF MS受限于数据库,不能鉴定到亚种的水平。结论本研究结果提示VITEK 2 Compact法不适用于克罗诺杆菌属种的鉴定;全基因组测序鉴定结果准确可靠;MALDI-TOF MS可以实现快速、高通量、准确的鉴定,仍需要进一步研究克罗诺杆菌属3个亚种的蛋白指纹图谱特点,丰富蛋白指纹图谱数据库,使其能够准确鉴定克罗诺杆菌属的7个种和3个亚种。     

Technical note: Use of transfer RNA-intergenic spacer PCR combined with capillary electrophoresis to identify coagulase-negative Staphylococcus species originating from bovine milk and teat apices

Coagulase-negative staphylococci (CNS) are the most frequently isolated bacteria in milk samples from cows with and without mastitis. Elucidating their relevance in bovine udder health is hampered because identification at the species level, if done at all, used to be performed based on phenotypic features. To provide a rapid, cheap, and easy-to-use genotypic technique that can be used to identify CNS species from milk and teat apices from cows, the performance of transfer RNA-intergenic spacer PCR (tDNA-PCR) in combination with capillary electrophoresis was evaluated. After updating the tDNA library with CNS reference strains, 288 field isolates were identified with tDNA-PCR and gene sequencing, and the latter was used as the reference method. The field isolates were divided in 2 groups of 144. Isolates of the first group were identified with tDNA-PCR with a typeability of 81.9% and an accuracy of 94.1%. Peak patterns of these isolates were then added to the tDNA library with species identity as determined by DNA sequencing. The second group was identified with the updated tDNA library, resulting in 91.0% typeability and 99.2% accuracy. This study showed that the updated tDNA-PCR in combination with capillary electrophoresis was almost as accurate as gene sequencing but faster and cheaper (only $3 per isolate), and is a useful tool in observational studies concerning the epidemiology of bovine CNS species.     

Microbial diversity during maturation and natural processing of coffee cherries of Coffea arabica in Brazil

The magnitude and diversity of the microbial population associated with dry (natural) processing of coffee (Coffea arabica) has been assessed during a 2-year period on 15 different farms in the Sul de Minas region of Brazil. Peptone water-washed samples were taken of maturing cherries on trees (cherries, raisins and dried cherries) and from ground fermentations. The microbial load varied from 3×10⁴ to 2.2×10⁹ cfu/cherry with a median value of 1.6×10⁷ cfu/cherry. The microbial load increased after heavy rainfall on cherries that were drying on the ground. At all stages, bacteria were usually the most abundant group, followed by filamentous fungi and finally yeasts. Counts of bacteria, yeasts and fungi varied considerably between farms and at different stages of maturation and processing and no consistent pattern could be seen. Yeasts showed an increase during the fermentation process. Median counts were not significantly different for fungi, yeasts and bacteria between the 2 years although Gram-negative bacteria dominated in the wet year and Gram-positive bacteria dominated in the dry year. Of a total of 754 isolates, 626 were identified to at least genus level comprising 44 genera and 64 different species. The 164 isolates of Gram-negative bacteria included 17 genera and 26 species, the most common of which were members of the genera Aeromonas, Pseudomonas, Enterobacter and Serratia. Of 191 isolates of Gram-positive bacteria, 23 were spore-forming and included six Bacillus species, and 118 were non-spore-formers of which over half were Cellulomonas with lesser numbers of Arthrobacter, Microbacterium, Brochothrix, Dermabacter and Lactobacillus. Of the 107 yeast isolates, 90 were identified into 12 genera and 24 different species and almost all were fermentative. The most common genera, in decreasing frequency, were Pichia, Candida, Arxula and Saccharomycopsis. There were many rarely described yeasts including Pichia lynferdii and Arxula adeninivorans. Almost all 292 fungal isolates were identified to genus level and 52 were identified to species level. Cladosporium, Fusarium and Penicillium each comprised about one third of the isolates and were found on all farms. Only 3% of the isolates were Aspergillus. Beauvaria, Monilia, Rhizoctonia and Arthrobotrys species were also occasionally found. The microbial flora is much more varied and complex than found in wet fermentations. The genera and species identified include members known to have all types of pectinase and cellulase activities.