Clinical relevance of positive intraoperative bacterial culture in tibial plateau leveling osteotomy in dogs: a retrospective study.

BACKGROUND: Tibial plateau leveling osteotomy (TPLO) belongs to the most frequently used surgical method for the treatment of cranial cruciate ligament rupture in dogs. Surgical site infection (SSI) is one of the possible postoperative complications. The aim of this study was to evaluate the diagnostic value of intraoperative bacterial culture as a tool for the detection of intraoperative bacterial contamination progressing to infection development in canine TPLO. Electronic patient records from dogs who underwent TPLO between January 2018 to December 2020 were retrospectively reviewed. Intraoperative bacterial culture results, used antimicrobial drugs and presence of SSI were recorded. RESULTS: Ninety-eight dogs were included in the study. SSI rate was 10.2%. All dogs who developed SSI (n = 10) had negative intraoperative bacterial cultures. None of the dogs with positive intraoperative bacterial culture (n = 6) developed SSI. The most cultured bacteria causing SSI was Staphylococcus pseudintermedius (n = 4). CONCLUSIONS: Intraoperative bacterial culture in dogs undergoing TPLO is not suitable as a predictor of surgical site infection.

Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs.

Human cutaneous squamous cell carcinomas (SCCs) and actinic keratoses (AK) display microbial dysbiosis with an enrichment of staphylococcal species, which have been implicated in AK and SCC progression. SCCs are common in both felines and canines and are often diagnosed at late stages leading to high disease morbidity and mortality rates. Although recent studies support the involvement of the skin microbiome in AK and SCC progression in humans, there is no knowledge of this in companion animals. Here, we provide microbiome data for SCC in cats and dogs using culture-independent molecular profiling and show a significant decrease in microbial alpha diversity on SCC lesions compared to normal skin (P ≤ 0.05). Similar to human skin cancer, SCC samples had an elevated abundance of staphylococci relative to normal skin-50% (6/12) had >50% staphylococci, as did 16% (4/25) of perilesional samples. Analysis of Staphylococcus at the species level revealed an enrichment of the pathogenic species Staphylococcus felis in cat SCC samples, a higher prevalence of Staphylococcus pseudintermedius in dogs, and a higher abundance of Staphylococcus aureus compared to normal skin in both companion animals. Additionally, a comparison of previously published human SCC and perilesional samples against the present pet samples revealed that Staphylococcus was the most prevalent genera across human and companion animals for both sample types. Similarities between the microbial profile of human and cat/dog SCC lesions should facilitate future skin cancer research. IMPORTANCE: The progression of precancerous actinic keratosis lesions (AK) to cutaneous squamous cell carcinoma (SCC) is poorly understood in humans and companion animals, despite causing a significant burden of disease. Recent studies have revealed that the microbiota may play a significant role in disease progression. Staphylococcus aureus has been found in high abundance on AK and SCC lesions, where it secretes DNA-damaging toxins, which could potentiate tumorigenesis. Currently, a suitable animal model to investigate this relationship is lacking. Thus, we examined the microbiome of cutaneous SCC in pets, revealing similarities to humans, with increased staphylococci and reduced commensals on SCC lesions and peri-lesional skin compared to normal skin. Two genera that were in abundance in SCC samples have also been found in human oral SCC lesions. These findings suggest the potential suitability of pets as a model for studying microbiome-related skin cancer progression.

Coagulase-negative staphylococci are the main causes of bacterial meningitis in duck.

Since September 2018, serious meningitis has been found on some breeding-duck farms in Shandong Province, China. A large number of ducks exhibit severe neurological symptoms. The ducks were randomly selected for laboratory testing. Duck brain samples were collected using standard sterile techniques, and the staphylococci isolates were detected in 404 (70.14%) out of 576 brain samples. A total of 525 coagulase-negative staphylococci (CoNS) strains were isolated, including 6 species: Staphylococcus sciuri (S. sciuri) (67.24%, 353/525), Staphylococcus epidermidis (S. epidermidis) (9.71%, 51/525), Staphylococcus saprophyticus (S. saprophyticus) (8.38%, 44/525), Staphylococcus lentus (S. lentus) (7.62%, 40/525), Staphylococcus haemolyticus (S. haemolyticus) (2.48%, 13/525), and Staphylococcus xylosus (S. xylosus) (4.57%, 24/525). Mixed strain infections were detected in 121 (29.95%) infected presentations. The antimicrobial susceptibility testing indicated that 40.38% of the isolates exhibited multi-drug resistance, and 53.90% of the strains were methicillin-resistant strains by amplification of the methicillin resistance gene (mecA) gene. Through experimental reproduction of the disease, we determined that the CoNS strains were the leading pathogens causing bacterial meningitis in ducks. Although these CoNS strains does not directly cause the death of sick ducks, they still cause large economic losses due to the retarded growth and development of the sick ducks, lower feed returns, and lower grades of processed duck products. The results of this study will contribute to our understanding of the epidemiology and pathogenesis of CoNS and be helpful in the prevention and treatment of the infection.

High α-diversity of skin microbiome and mycobiome in Japanese patients with vitiligo.

BACKGROUND: Vitiligo is an acquired pigmentary disorder characterized by depigmented patches on the skin that majorly impact patients' quality of life. Although its etiology involves genetic and environmental factors, the role of microorganisms as environmental factors in vitiligo pathology remains under-researched. OBJECTIVES: Our study explored the presence of characteristic bacterial and fungal flora in vitiligo-affected skin and investigated their potential roles in vitiligo pathogenesis. METHODS: We sequenced bacterial 16S rRNA and the fungal ITS1 region from skin swabs collected at frequently affected sites, namely the forehead and back, of patients with vitiligo. We analyzed bacterial and fungal flora in lesional and non-lesional areas of patients with vitiligo compared with corresponding sites in age- and sex-matched healthy subjects. RESULTS: Our findings revealed elevated α-diversity in both bacterial and fungal flora within vitiligo lesions compared with healthy controls. Notably, bacterial flora exhibited a distinctive composition in patients with vitiligo, and the proportional representation of Enterococcus was inversely correlated with the degree of vitiligo progression. Gammaproteobacteria, Staphylococcus spp., and Corynebacterium spp. were more abundant in vitiligo patients, with notable Staphylococcus spp. prevalence during the stable phase on the forehead. Conversely, the proportion of Malassezia sympodialis was lower and that of Malassezia globosa was higher in the progressive phase on the back of vitiligo patients. CONCLUSION: Our study identified some characteristic bacterial and fungal groups associated with vitiligo activity and prognosis, highlighting the potential roles of microorganisms in pathogenesis and offering insights into personalized disease-management approaches.

Description of Staphylococcal Strains from Straw-Coloured Fruit Bat (Eidolon helvum) and Diamond Firetail (Stagonopleura guttata) and a Review of their Phylogenetic Relationships to Other Staphylococci.

The phylogenetic tree of the Staphylococcus aureus complex consists of several distinct clades and the majority of human and veterinary S. aureus isolates form one large clade. In addition, two divergent clades have recently been described as separate species. One was named Staphylococcus argenteus, due to the lack of the "golden" pigment staphyloxanthin. The second one is S. schweitzeri, found in humans and animals from Central and West Africa. In late 2021, two additional species, S. roterodami and S. singaporensis, have been described from clinical samples from Southeast Asia. In the present study, isolates and their genome sequences from wild Straw-coloured fruit bats (Eidolon helvum) and a Diamond firetail (Stagonopleura guttata, an estrildid finch) kept in a German aviary are described. The isolates possessed staphyloxanthin genes and were closer related to S. argenteus and S. schweitzeri than to S. aureus. Phylogenetic analysis revealed that they were nearly identical to both, S. roterodami and S. singaporensis. We propose considering the study isolates, the recently described S. roterodami and S. singaporensis as well as some Chinese strains with MLST profiles stored in the PubMLST database as different clonal complexes within one new species. According to the principle of priority we propose it should be named S. roterodami. This species is more widespread than previously believed, being observed in West Africa, Southeast Asia and Southern China. It has a zoonotic connection to bats and has been shown to be capable of causing skin and soft tissue infections in humans. It is positive for staphyloxanthin, and it could be mis-identified as S. aureus (or S. argenteus) using routine procedures. However, it can be identified based on distinct MLST alleles, and "S. aureus" sequence types ST2470, ST3135, ST3952, ST3960, ST3961, ST3963, ST3965, ST3980, ST4014, ST4075, ST4076, ST4185, ST4326, ST4569, ST6105, ST6106, ST6107, ST6108, ST6109, ST6999 and ST7342 belong to this species.

Staphylococcus taiwanensis sp. nov., isolated from human blood.

A novel coagulase-negative Staphylococcus strain (NTUH-S172T) was isolated from human blood culture in Taiwan with preliminary identification of Staphylococcus saprophyticus. 16S rRNA gene analysis and multilocus sequence analysis (MLSA) showed that NTUH-S172T was most closely related to Staphylococcus haemolyticus. The average nucleotide identity and digital DNA-DNA hybridization values with the whole genome sequence were <95 % and<70 % when compared to the related species. Strain NTUH-S172T could be distinguished from S. haemolyticus by urease production and from Staphylococcus borealis by nitrate reduction. In addition, the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) spectrum of NTHU-S172T was significantly different from that of S. haemolyticus, which could be used in clinical identification. In conclusion, it is proposed that this isolate represents a novel species, named Staphylococcus taiwanensis sp. nov., with type strain NTUH-S172T (=BCRC 81315T=JCM 34726T).

Trends of Antimicrobial Susceptibility in Clinically Significant Coagulase-Negative Staphylococci Isolated from Cerebrospinal Fluid Cultures in Neurosurgical Adults: a Nine-Year Analysis.

Coagulase-negative staphylococci (CoNS) are the main pathogens in health care-associated ventriculitis and meningitis (HCAVM). This study aimed to assess antimicrobial susceptibility. Moreover, the treatment and clinical outcome were described. All neurosurgical adults admitted to one of the largest neurosurgical centers in China with clinically significant CoNS isolated from cerebrospinal fluid cultures in 2012 to 2020 were recruited. One episode was defined as one patient with one bacterial strain. Interpretive categories were applied according to the MICs. The clinical outcomes were dichotomized into poor (Glasgow Outcome Scale 1 to 3) and acceptable (Glasgow Outcome Scale 4 to 5). In total, 534 episodes involving 519 patients and 16 bacteria were analyzed. Over the 9 years, eight antimicrobial agents were used in antimicrobial susceptibility tests, including six in over 80% of CoNS. The range of resistance rates was 0.8% to 84.6%. The vancomycin resistance rate was the lowest, whereas the penicillin resistance rate was the highest. The linezolid (a vancomycin replacement) resistance rate was 3.1%. The rate of oxacillin resistance, representing methicillin-resistant staphylococci, was 70.2%. There were no significant trends of antimicrobial susceptibility over the 9 years for any agents analyzed. However, there were some apparent changes. Notably, vancomycin-resistant CoNS appeared in recent years, while linezolid-resistant CoNS appeared early and disappeared in recent years. Vancomycin (or norvancomycin), the most common treatment agent, was used in 528 (98.9%) episodes. Finally, 527 (98.7%) episodes had acceptable outcomes. It will be safe to use vancomycin to treat CoNS-related HCAVM in the immediate future, although continuous monitoring will be needed. IMPORTANCE Coagulase-negative staphylococci are the main pathogens in health care-associated ventriculitis and meningitis. There are three conclusions from the results of this study. First, according to antimicrobial susceptibility, the rates of resistance to primary antimicrobial agents are high and those to high-level agents, including vancomycin, are low. Second, the trends of resistance rates are acceptable, especially for high-level agents, although long-term and continuous monitoring is necessary. Finally, the clinical outcomes of neurosurgical adults with coagulase-negative staphylococci-related health care-associated ventriculitis and meningitis are acceptable after treatment with vancomycin. Therefore, according to the antimicrobial susceptibility and clinical practice, vancomycin will be safe to treat coagulase-negative staphylococci-related health care-associated ventriculitis and meningitis.

One Day in Denmark: Nationwide point-prevalence survey of human bacterial isolates and comparison of classical and whole-genome sequence-based species identification methods.

OBJECTIVES: Implementing whole-genome sequencing (WGS) technologies in clinical microbiology laboratories can increase the amount and quality of information available for healthcare practitioners. In this study, we analysed the applicability of this method and determined the distribution of bacterial species processed in clinical settings in Denmark. METHODS: We performed a point-prevalence study of all bacterial isolates (n = 2,009) processed and reported in the Clinical Microbiology Laboratories in Denmark in one day in January 2018. We compared species identification as performed by classical methods (MALDI-TOF) and by bioinformatics analysis (KmerFinder and rMLST) of WGS (Illumina NextSeq) data. We compared the national point-prevalence of bacterial isolates observed in clinical settings with the research attention given to those same genera in scientific literature. RESULTS: The most prevalent bacterium was Escherichia coli isolated from urine (n = 646), followed by Staphylococcus spp. from skin or soft tissues (n = 197). The distribution of bacterial species throughout the country was not homogeneous. We observed concordance of species identification for all methods in 95.7% (n = 1,919) of isolates, furthermore obtaining concordance for 99.7% (n = 1,999) at genus level. The number of scientific publications in the country did not correlate with the number of bacterial isolates of each genera analysed in this study. CONCLUSIONS: WGS technologies have the potential to be applied in clinical settings for routine diagnostics purposes. This study also showed that bioinformatics databases should be continuously improved and results from local point-prevalence surveys should not be applied at national levels without previously determining possible regional variations.

Effect of delayed entry of blood culture bottles in BACTEC automated blood culture system in the context of laboratory consolidation.

Delayed entry of blood culture bottles is frequent in consolidated laboratories. A retrospective study evaluated time from insertion to detection and total detection time as a function of preincubation time, and we prospectively looked for false negative results. 69,604 blood culture bottles were reviewed for preincubation time, incubation time and total detection time. Positive cultures for specific bacterial subtypes were reviewed to assess the effect of preincubation time on likelihood of detection. 492 negative blood cultures were prospectively tested by 16S RNA PCR and Staphylococcus-specific PCR for the presence of bacterial DNA. Mean preincubation time for samples collected within the city-limits was 3.94 h versus 9.49-18.89 h for other client sites. Higher preincubation times were partially mitigated by a lower incubation time, with an overall increase in total detection time. A lower odds ratio of recovery of Staphylococcus spp was identified, but not confirmed by terminal subcultures and molecular assays. Prolonged preincubation of blood cultures affects total detection time despite a reduction in incubation time. Successful centralization of microbiological services may depend upon optimization of courier routes for inoculated blood culture bottles. Our data supports consideration for an increase in suggested maximum preincubation times.

Species identification and antimicrobial susceptibility profile of bacteria associated with cow mastitis in southern Brazil / Identificação de espécies e perfil de suscetibilidade aos antimicrobianos de bactérias associadas à mastite bovina no sul do Brasil

Bovine mastitis is the most common disease in dairy cattle and responsible for economic losses in the milk industry. The present study aimed to identify the main species and to evaluate the antimicrobial susceptibility of bacterial isolates from cow herds with mastitis in dairy farms from southern Brazil. A total of 107 milk samples were collected from different cow herds in one important dairy producing region in southern Brazil, including farms located in ten cities from the Northeast region in the Rio Grande do Sul state. Bacterial strains were isolated and submitted to presumptive identification by classical bacteriological methods. Bacterial species were also identified by MALDI-TOF MS and antimicrobial susceptibility testing was performed with 12 antimicrobials commonly used in dairy farms. Fifty-one bacterial strains were isolated and the presumptive identification demonstrated the occurrence of Staphylococcus spp. (82.3%), Bacillus spp. (3.9%), Klebsiella spp. (3.9%), Streptococcus spp. (3.9%), Corynebacterium sp. (2%), Enterococcus sp. (2%) and Serratia sp. (2%). Forty-one isolates were successfully identified in the MALDI-TOF analysis, including 35 isolates from eleven different bacterial species. Importantly, there were eight different Staphylococcus species, with a high frequency of Staphylococcus chromogenes (48.6%) and Staphylococcus aureus (20%). Overall, bacterial isolates demonstrated resistance to penicillin (46.3%), tetracycline (39%), amoxicillin (36.6%), ampicillin (34.1%) and sulfamethoxazole/trimethoprim (31.7%). Enrofloxacin was the unique antimicrobial that all isolates were susceptible. In addition, there were six multidrug resistant isolates (five S. chromogenes and one S. aureus). This study highlights that bacterial pathogens with resistance to several antimicrobials were identified in cows from dairy farms in a very important milk producing region located in southern Brazil. Microbial identification of the bovine mastitis pathogens and determination of the antimicrobial profile is necessary for the rational use of the medicines.(AU)

A mastite bovina é a doença mais comum em gado leiteiro e responsável por perdas econômicas na indústria de laticínios. O presente estudo teve como objetivo identificar as principais espécies e avaliar a suscetibilidade antimicrobiana de isolados bacterianos de rebanhos bovinos com mastite em fazendas leiteiras no sul do Brasil. Um total de 107 amostras de leite foram coletadas em diferentes rebanhos bovinos em uma importante região produtora de leite do sul do Brasil, incluindo fazendas localizadas em 10 cidades da região Nordeste do estado do Rio Grande do Sul. As cepas bacterianas foram isoladas e submetidas à identificação presuntiva por métodos bacteriológicos clássicos. A identificação bacteriana foi confirmada por MALDI-TOF MS e o teste de sensibilidade antimicrobiana foi realizado com antimicrobianos comumente usados em fazendas leiteiras. Cinquenta e uma cepas bacterianas foram isoladas e a identificação presuntiva demonstrou a ocorrência de Staphylococcus spp. (82,3%), Bacillus spp. (3,9%), Klebsiella spp. (3,9%), Streptococcus spp. (3,9%), Corynebacterium sp. (2%), Enterococcus sp. (2%) e Serratia sp. (2%). Os 41 isolados foram identificados com sucesso na análise MALDI-TOF, incluindo 35 isolados de onze espécies bacterianas diferentes. É importante ressaltar que houve a ocorrência de oito espécies diferentes de Staphylococcus, com alta frequência de Staphylococcus chromogenes (48,6%) e Staphylococcus aureus (20%). No geral, os isolados bacterianos tiveram alta resistência à penicilina (46,3%), tetraciclina (39%), amoxicilina (36,6%), ampicilina (34,1%) e sulfametoxazol/trimetoprima (31,7%). A enrofloxacina foi o único antimicrobiano que todos os isolados foram suscetíveis. Além disso, havia seis isolados multirresistentes (cinco S. chromogenes e um S. aureus). Este estudo destaca que os patógenos bacterianos com resistência aos antimicrobianos estão presentes em fazendas leiteiras de subsistência em uma importante região produtora no sul do Brasil. É necessário o monitoramento constante dos patógenos da mastite bovina e a determinação de seu perfil antimicrobiano para o uso racional dos medicamentos.(AU)

Species identification and antimicrobial susceptibility profile of bacteria associated with cow mastitis in southern Brazil / Identificação de espécies e perfil de suscetibilidade aos antimicrobianos de bactérias associadas à mastite bovina no sul do Brasil

Bovine mastitis is the most common disease in dairy cattle and responsible for economic losses in the milk industry. The present study aimed to identify the main species and to evaluate the antimicrobial susceptibility of bacterial isolates from cow herds with mastitis in dairy farms from southern Brazil. A total of 107 milk samples were collected from different cow herds in one important dairy producing region in southern Brazil, including farms located in ten cities from the Northeast region in the Rio Grande do Sul state. Bacterial strains were isolated and submitted to presumptive identification by classical bacteriological methods. Bacterial species were also identified by MALDI-TOF MS and antimicrobial susceptibility testing was performed with 12 antimicrobials commonly used in dairy farms. Fifty-one bacterial strains were isolated and the presumptive identification demonstrated the occurrence of Staphylococcus spp. (82.3%), Bacillus spp. (3.9%), Klebsiella spp. (3.9%), Streptococcus spp. (3.9%), Corynebacterium sp. (2%), Enterococcus sp. (2%) and Serratia sp. (2%). Forty-one isolates were successfully identified in the MALDI-TOF analysis, including 35 isolates from eleven different bacterial species. Importantly, there were eight different Staphylococcus species, with a high frequency of Staphylococcus chromogenes (48.6%) and Staphylococcus aureus (20%). Overall, bacterial isolates demonstrated resistance to penicillin (46.3%), tetracycline (39%), amoxicillin (36.6%), ampicillin (34.1%) and sulfamethoxazole/trimethoprim (31.7%). Enrofloxacin was the unique antimicrobial that all isolates were susceptible. In addition, there were six multidrug resistant isolates (five S. chromogenes and one S. aureus). This study highlights that bacterial pathogens with resistance to several antimicrobials were identified in cows from dairy farms in a very important milk producing region located in southern Brazil. Microbial identification of the bovine mastitis pathogens and determination of the antimicrobial profile is necessary for the rational use of the medicines.

A mastite bovina é a doença mais comum em gado leiteiro e responsável por perdas econômicas na indústria de laticínios. O presente estudo teve como objetivo identificar as principais espécies e avaliar a suscetibilidade antimicrobiana de isolados bacterianos de rebanhos bovinos com mastite em fazendas leiteiras no sul do Brasil. Um total de 107 amostras de leite foram coletadas em diferentes rebanhos bovinos em uma importante região produtora de leite do sul do Brasil, incluindo fazendas localizadas em 10 cidades da região Nordeste do estado do Rio Grande do Sul. As cepas bacterianas foram isoladas e submetidas à identificação presuntiva por métodos bacteriológicos clássicos. A identificação bacteriana foi confirmada por MALDI-TOF MS e o teste de sensibilidade antimicrobiana foi realizado com antimicrobianos comumente usados em fazendas leiteiras. Cinquenta e uma cepas bacterianas foram isoladas e a identificação presuntiva demonstrou a ocorrência de Staphylococcus spp. (82,3%), Bacillus spp. (3,9%), Klebsiella spp. (3,9%), Streptococcus spp. (3,9%), Corynebacterium sp. (2%), Enterococcus sp. (2%) e Serratia sp. (2%). Os 41 isolados foram identificados com sucesso na análise MALDI-TOF, incluindo 35 isolados de onze espécies bacterianas diferentes. É importante ressaltar que houve a ocorrência de oito espécies diferentes de Staphylococcus, com alta frequência de Staphylococcus chromogenes (48,6%) e Staphylococcus aureus (20%). No geral, os isolados bacterianos tiveram alta resistência à penicilina (46,3%), tetraciclina (39%), amoxicilina (36,6%), ampicilina (34,1%) e sulfametoxazol/trimetoprima (31,7%). A enrofloxacina foi o único antimicrobiano que todos os isolados foram suscetíveis. Além disso, havia seis isolados multirresistentes (cinco S. chromogenes e um S. aureus). Este estudo destaca que os patógenos bacterianos com resistência aos antimicrobianos estão presentes em fazendas leiteiras de subsistência em uma importante região produtora no sul do Brasil. É necessário o monitoramento constante dos patógenos da mastite bovina e a determinação de seu perfil antimicrobiano para o uso racional dos medicamentos.

Composition of nasal bacterial community and its seasonal variation in health care workers stationed in a clinical research laboratory.

The microorganisms at the workplace contribute towards a large portion of the biodiversity a person encounters in his or her life. Health care professionals are often at risk due to their frontline nature of work. Competition and cooperation between nasal bacterial communities of individuals working in a health care setting have been shown to mediate pathogenic microbes. Therefore, we investigated the nasal bacterial community of 47 healthy individuals working in a clinical research laboratory in Kuwait. The taxonomic profiling and core microbiome analysis identified three pre-dominant genera as Corynebacterium (15.0%), Staphylococcus (10.3%) and, Moraxella (10.0%). All the bacterial genera exhibited seasonal variations in summer, winter, autumn and spring. SparCC correlation network analysis revealed positive and negative correlations among the classified genera. A rich set of 16 genera (q < 0.05) were significantly differentially abundant (LEfSe) across the four seasons. The highest species counts, richness and evenness (P < 0.005) were recorded in autumn. Community structure profiling indicated that the entire bacterial population followed a seasonal distribution (R2-0.371; P < 0.001). Other demographic factors such as age, gender and, ethnicity contributed minimally towards community clustering in a closed indoor laboratory setting. Intra-personal diversity also witnessed rich species variety (maximum 6.8 folds). Seasonal changes in the indoor working place in conjunction with the outdoor atmosphere seems to be important for the variations in the nasal bacterial communities of professionals working in a health care setting.

Dynamics of the urinary microbiome in pregnancy and the coincidental predictive value of the microbiota for IVF/IVF-ICSI outcome.

RESEARCH QUESTION: What is the impact of clinical pregnancy on the composition of the urinary microbiota? DESIGN: Eighty-five women receiving IVF, without or with intracytoplasmic sperm injection (ICSI) treatment were enrolled in a prospective observational study performed in 2008. Approximately 14 weeks before the start of hormonal treatment and embryo transfer, a midstream urine sample was obtained, followed by an additional sample 16 weeks after embryo transfer. The microbial composition was determined by polymerase chain reaction of the V1-V3 regions of the 16S rRNA bacterial gene. Clinical pregnancy data were collected after the first IVF/IVF-ICSI cycle and 1 year later. RESULTS: A significant decrease in the abundance of Lactobacillus species as well as a significant increase in that of Staphylococcus species was observed in women who became pregnant after IVF/IVF-ICSI treatment (both P < 0.0001). In addition, based on the composition of the pretreatment microbiome it was possible to identify women with a lower likelihood of achieving clinical pregnancy after IVF/IVF-ICSI treatment. The resulting prediction model was validated in another 27 women who did not become pregnant during the first cycle and received additional IVF/IVF-ICSI cycle(s) or frozen embryo transfer(s). The model predicted the women with no clinical pregnancy after IVF/IVF-ICSI treatment with a sensitivity of 0.42 and a specificity of 1.00. CONCLUSIONS: The data primarily showed that clinical pregnancy results in significant changes in the abundance and diversity of the urinary microbiota. Coincidentally, it was discovered that the urinary microbiome composition before IVF/IVF-ICSI treatment can potentially be used as a predictor of clinical pregnancy.

Staphylococcus singaporensis sp. nov., a new member of the Staphylococcus aureus complex, isolated from human clinical specimens.

Staphylococcus argenteus and Staphylococcus schweitzeri are the newest members of the Staphylococcus aureus complex. The number of clinical reports attributed to these new S. aureus complex members is limited. In a retrospective clinical laboratory study conducted over a 4-month period investigating the prevalence of S. argenteus and S. schweitzeri, a total of 43 isolates were selected. Phylogeny based on core-gene multilocus sequence typing (MLST) analysis confirmed that 37 were S. argenteus but a genetically distinct clade of six isolates was identified. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses further supported the classification of these six isolates as a separate species. When compared to S. aureus complex reference genomes, the ANI values were ≤94 % and the dDDH values were <53 %. Based on the seven-gene S. aureus MLST scheme, the six isolates belong to five novel allelic profiles (ST6105, ST6106, ST6107, ST6108 and ST109). Their clinical infection features were similar to S. aureus. Skin and soft tissue infections presented in four out of the six cases. Routine clinical diagnostic identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and biochemical profiling does not differentiate these new members from the rest of the complex. Genotypic analysis suggests that the six isolates belong to a novel species, Staphylococcus singaporensis sp. nov. with isolate SS21T (=DSM 111408T=NCTC14419T) designated as the type strain.

Epidemiology of Staphylococcus pseudintermedius in cats in Poland.

Staphylococcus pseudintermedius is a well-known coagulase-positive staphylococcus that is mainly associated with the asymptomatic colonization of the skin of pets and mucous membranes. Little is still known about the occurrence of S. pseudintermedius in cats. The current study aimed to characterize the isolates of S. pseudintermedius from sick and healthy cats. This was achieved by examining their antibiotic resistance properties, biofilm formation, and genotype differences. Six hundred and seventy-six cats were swabbed (595 healthy and 81 sick cats). Thirty-five distinct S. pseudintermedius isolates from 27 cats were isolated. The prevalence of S. pseudintermedius in healthy and sick cats was 2.49% and 7.61%, respectively. In comparison, MRSP (methicillin-resistant Staphylococcus pseudintermedius) prevalence was 0.12% and 2.98%, respectively. Cats were more frequently colonized with S. pseudintermedius when kept with dogs, regardless of their health condition, with this result being statistically significant. Multidrug resistance was detected in 50%, and 38.46% of S. pseudintermedius isolates from healthy and sick cats, respectively. In contrast, genetic multidrug resistance was detected in 59% and 46.15% cases, respectively. Seven from eight isolated MRSPs were multidrug-resistant. Multi-locus sequence typing (MLST) assigned isolates to 19 types, of which 16 types submitted for the first time to the PubMLST database. The most frequently detected STs (sequence types) were 551 and 71. ST71 and ST551 were mainly isolated from cats with clinical signs of infection. All were MRSPs, regardless of cats' health. These isolates were characterized with the most frequent antibiotic resistance at the phenotypic and genotypic level.

Simple indictor of increased blood culture contamination rate by detection of coagulase-negative staphylococci.

Coagulase-negative staphylococci (CoNS) are the most frequent contaminating bacteria; therefore, we aimed to investigate an indicator of CoNS to predict the increase in blood culture contamination rate (ConR). We performed a retrospective study of selected patients, who underwent blood culture testing. Contamination was defined as the presence of either one of two or more sets of skin-resident bacteria, except for cases with a low likelihood of contamination based on clinical aspects. We calculated the monthly ConR [(total number of contaminated cases per month)/(total number of blood culture sets collected per month) × 100] and analysed the ConR prediction ability using the following four indicators: the number of CoNS-positive sets of blood cultures, cases with at least one CoNS-positive blood culture set, cases with only one CoNS-positive blood culture set, and cases of contamination by CoNS. Cases with CoNS-positive blood cultures correlated with ConR (r = 0.85). Although the area under the receiver operating characteristic curve for the number of cases with ConR ≥ 2.5 differed significantly from that of the number of cases contaminated by CoNS, the negative predictive value was high, reaching up to 95.5% (95% confidential interval 87.3-99.1). The number of CoNS-positive cases could help predict an increase in ConR ≥ 2.5.

In vitro activity of dalbavancin and other anti-staphylococcal agents against infecting isolates of methicillin-resistant coagulase-negative staphylococci.

Introduction. Dalbavancin was approved in Europe in 2015 for skin and soft tissue infections.Hypothesis/Gap Statement. Data on methicillin-resistant coagulase-negative staphylococci (MR-CNS) dalbavancin susceptibility are scarce.Aim. To assess the susceptibility of MR-CNS to dalbavancin and other anti-staphylococcal agents.Methodology. A total of 443 MR-CNS clinical isolates from patients hospitalized in a Greek university hospital during a 2.5-year period (January 2018 to June 2020) were included. The MICs for vancomycin, teicoplanin, linezolid and daptomycin were investigated by Etest and the MIC for dalbavancin was determined according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines in 196 isolates. The consumption of the aforementioned antimicrobials was calculated.Results. In total, 51 isolates were resistant to teicoplanin (11.5 %) and 211 (47.6 %) to linezolid; all were susceptible to vancomycin and daptomycin. Among 196 isolates tested, 32 (16.3 %) were resistant to dalbavancin. A significant increase of MIC during the study period was found for vancomycin, teicoplanin and daptomycin, while a decrease in linezolid's MIC was observed. Dalbavancin's MIC remained stable. No difference in consumption was observed among the studied anti-staphylococcal agents.Conclusion. An increase of vancomycin, teicoplanin and daptomycin MICs among MR-CNS was observed, whereas 47.6 % of isolates were non-susceptible to linezolid. Dalbavancin retains excellent potency against MR-CNS, even in the presence of non-susceptibility to other anti-staphylococcal antibiotics.

First human case of catheter-related blood stream infection caused by Staphylococcus schleiferi subspecies coagulans: a case report and literature review.

BACKGROUND: Staphylococcus schleiferi is a gram-positive pathogenic coccus which causes canine skin and ear infections. Only four cases of human infection caused by Staphylococcus schleiferi subspecies coagulans have been reported. Herein, we present the first case of catheter-related bloodstream infection caused by S. schleiferi subspecies coagulans. CASE PRESENTATION: A 62-year-old Japanese man was admitted to our hospital for examination of sigmoid colon tumor. During hospitalization, he had fever, shaking chills, and swelling at the peripheral venous catheter insertion site. Two sets of blood cultures were positive for S. schleiferi subspecies coagulans which was confirmed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), 16S ribosomal RNA sequencing and the coagulase test. The patient was successfully treated without relapse. CONCLUSION: To our knowledge, this is the first report of catheter-related bloodstream infection caused by S. schleiferi subspecies coagulans. S. schleiferi subsp. coagulans can be pathogenic in humans, and MALDI-TOF MS can contribute to accurate identification of S. schleiferi subspecies coagulans.

Extensive countrywide field investigation of somatic cell counts and total bacterial counts in bulk tank raw milk in goat herds in Greece.

Dairy goat farming is an important sector of the agricultural industry in Greece, with an annual total milk production exceeding 450 000 l and accounting for over 25% of all goat milk produced in the European Union; this milk is used mainly for cheese production. Despite the importance of goat milk for the agricultural sector in Greece, no systematic countrywide investigations in the bulk-tank milk of goats in Greece have been reported. Objectives were to investigate somatic cell counts (SCC) and total bacterial counts (TBC) in raw bulk-tank milk of goat herds in Greece, study factors influencing SCC and TBC therein and evaluate their possible associations with milk content. Throughout Greece, 119 dairy goat herds were visited for milk sampling for somatic cell counting, microbiological examination and composition measurement. Geometric mean SCC and TBC were 0.838 × 106 cells ml-1 and 581 × 103 cfu ml-1, respectively. Multivariable analyses revealed annual frequency of check-ups of milking system and total milk quantity per goat (among 53 variables) to be significant for increased SCC; no factor emerged (among 58 variables) to be significant for increased TBC. Negative correlation of SCC with total protein was found; mean total protein content in the bulk-tank milk in herds with SCC >0.75 × 106 cells ml-1 was 5.1% lower and in herds with SCC >1.5 × 106 cells ml-1, it was 7.8% lower.

Occurrence and aetiology of subclinical mastitis in water buffalo in Bangladesh.

Subclinical mastitis (SCM) in water buffalo is a production disease associated with decreased milk yield and impaired milk quality and safety. Water buffalo is an important livestock species in Bangladesh, but information about the occurrence and aetiology of SCM in this species is scarce. A cross-sectional study was conducted as part of the Udder Health Bangladesh Programme to (i) determine the occurrence of SCM and bulk milk somatic cell count (SCC) in water buffalo in Bangladesh, (ii) identify pathogens causing SCM and (iii) evaluate penicillin resistance in isolated staphylococci strains. Sixteen buffalo farms in the Bagerhat and Noakhali regions of Bangladesh were selected for study and a bulk milk sample was collected from each farm. In addition, 299 udder quarter milk samples were collected from 76 animals. The bulk milk samples were assessed by direct SCC and the quarter milk samples by California mastitis test (CMT). The occurrence of SCM calculated at quarter and animal level was 42.5 and 81.6%, respectively. Milk samples from 108 CMT-positive quarters in 48 animals and 38 randomly selected CMT-negative quarters in 24 animals were investigated using bacteriological culture. Estimated mean bulk milk SCC was 195 000 cells/ml milk (range 47 000- 587 000 cells/ml milk). On culture, estimated quarter-level intramammary infection (IMI) was 40.4%. The identity of isolated bacteria was confirmed by MALDI-TOF mass spectrometry. Non-aureus staphylococci (NAS) were the most common pathogens (24.7%) and, among 36 NAS tested, 36.1% were resistant to penicillin. Thus there was high occurrence of SCM on the study farms, with relatively high penicillin resistance in NAS. Further studies are needed to identify underlying risk factors and develop an udder health control strategy for water buffalo in Bangladesh.