The unintended contribution of clinical microbiology laboratories to climate change and mitigation strategies: a combination of descriptive study, short survey, literature review and opinion.

OBJECTIVE: Climate change poses a significant threat to humanity and human activity is largely responsible for it. Clinical microbiology laboratories have their unintended shares in carbon dioxide (CO2) emissions. The aim of this study is to estimate CO2 emission of a clinical microbiology laboratory and to propose initiatives to reduce the emissions. METHODS: CO2 emission of instruments was estimated based on their electricity consumption. CO2 emitted in producing consumables was estimated by weighing the consumables needed to perform major tests in a large academic hospital. A systematic literature review was performed to identify studies on the impact of clinical microbiology laboratories on the environment. A short survey was sent to four major manufacturers of agar plates on initiatives to reduce the environmental impact of their products. Opinion was given on activities that can reduce CO2 emission in laboratories. RESULTS: The study shows that the largest amount of CO2 emission in the microbiological laboratories comes from consumables and personnel commuting. For example, the production and transportation of agar plates needed to culture samples for a year in a hospital with 1320 beds result in 16 590 kg CO2 is emitted. All survey participants mentioned that they were committed to reduce environmental impact of their products. The initiatives to reduce CO2 emission can be performed at the laboratory and at policy level, such as reducing the number of tests to only the necessary amount to reduce consumables. DISCUSSION: The calculations contribute to map CO2-related emissions in clinical microbiology laboratory activities, and the proposed initiatives to reduce the CO2 may serve as starting point for further discussions.

Cutaneous Brucellosis unmasked as Aureimonas altamirensis in a wound culture.

Aureimonas altamirensis was isolated from a wound culture and initially misidentified as Brucella melitensis by the VITEK® 2 system. The VITEK-MS did not provide identification whereas the Bruker MALDI-ToF MS system and 16-S sequencing revealed a clear identification, which highlights the importance of inclusion of species in databases for accurate and fast identification of bacteria.

The effect of extra safety measures on incidence of surgical site infection after alloplastic breast reconstruction.

BACKGROUND: This study aimed to evaluate whether the implementation of extra perioperative safety measures and precautions through adopted standard operating procedures (SOPs) to ensure optimal anti-microbial conditions has led to less surgical site infections (SSI) after alloplastic breast reconstruction (BR). METHODS: This retrospective study compared two Cohorts of patients treated before and after the implementation of new SOPs (2009-2014: Cohort 1 versus 2014-2019: Cohort 2). Multivariate logistic regression analyses, adjusting for patient confounders, were implemented to compare SSI incidence between both Cohorts. RESULTS: Overall, SSI incidence was equal in both groups (10%, p = 0.545). The incidence of deep SSI was 9% for Cohort 1 and 5% for Cohort 2 (p = 0.074). Incidence of SSI-related explantation was 8% and 5%, respectively (p = 0.136). After adjusting for patient confounders, no statistically significant difference was seen between both Cohorts in overall SSI, deep SSI incidence, and explantation due to SSI (ORadjusted: -0.31, p = 0.452, ORadjusted: 0.16, p = 0.747 and ORadjusted: 0.18, p = 0.712). Higher BMI, smoking, one-stage BR, and immediate BR were associated with the risk for SSI (p<0.001, p = 0.036, p<0.001, and p = 0.022, respectively). CONCLUSION: Extra safety measures to assure optimal anti-microbial conditions did not contribute to lower SSI incidence or SSI-related explantation after alloplastic BR. Confounders such as BMI, smoking, immediate BR, and one-stage BR were correlated to an increased risk for overall SSI, deep SSI, and SSI-related explantation of TE/implants.

Patients With Inflammatory Bowel Disease Show IgG Immune Responses Towards Specific Intestinal Bacterial Genera.

Introduction: Inflammatory bowel disease (IBD) is characterized by a disturbed gut microbiota composition. Patients with IBD have both elevated mucosal and serum levels of IgG-antibodies directed against bacterial antigens, including flagellins. In this study, we aimed to determine to which intestinal bacteria the humoral immune response is directed to in patients with IBD. Methods: Fecal and serum samples were collected from patients with IBD (n=55) and age- and sex-matched healthy controls (n=55). Fecal samples were incubated with autologous serum and IgG-coated fractions were isolated by magnetic-activated cell sorting (MACS) and its efficiency was assessed by flow cytometry. The bacterial composition of both untreated and IgG-coated fecal samples was determined by 16S rRNA-gene Illumina sequencing. Results: IgG-coated fecal samples were characterized by significantly lower microbial diversity compared to the fecal microbiome. Both in patients with IBD and controls, serum IgG responses were primarily directed to Streptococcus, Lactobacillus, Lactococcus, Enterococcus, Veillonella and Enterobacteriaceae, as well as against specific Lachnospiraceae bacteria, including Coprococcus and Dorea (all P<0.001), and to Ruminococcus gnavus-like bacteria (P<0.05). In contrast, serological IgG responses against typical commensal, anaerobic and colonic microbial species were rather low, e.g. to the Lachnospiraceae members Roseburia and Blautia, to Faecalibacterium, as well as to Bacteroides. Patients with IBD showed more IgG-coating of Streptococcus, Lactobacillus, and Lactococcus bacteria compared to healthy controls (all P<0.05). No differences in IgG-coated bacterial fractions were observed between Crohn's disease and ulcerative colitis, between active or non-active disease, nor between different disease locations. Conclusion: The IgG immune response is specifically targeted at distinct intestinal bacterial genera that are typically associated with the small intestinal microbiota, whereas responses against more colonic-type commensals are lower, which was particularly the case for patients with IBD. These findings may be indicative of a strong immunological exposure to potentially pathogenic intestinal bacteria in concordance with relative immune tolerance against commensal bacteria.