Local Microbiology Research Articles

Shipwrecks under the microscope: feeding the deep

The sediment of the deep sea is one of the largest ecosystems on the planet and also one of the least explored. The lack of light, high pressure and low temperature mean that only specialised organisms can inhabit these areas. These include microbes, often relying on any form of sustenance they can get, and what starts as just a cluster can form the base of biodiverse communities. Examples of deep-sea microbial hotspots include the areas around whale carcasses, which have been reasonably well studied, and wooden-hulled shipwrecks, both of which provide nutrition, a safe place to hide and surfaces to be colonised. However, the sites of shipwrecks have rarely been examined under the microscope. Justyna Hampel and colleagues from the University of Southern Mississippi, USA, and the US Bureau of Ocean Management examined two wooden-hulled deep-sea shipwrecks in the northern Gulf of Mexico: one relatively shallow (∼525 m) and one deep (∼1800 m), both from the late 19th century.To describe the microbial ecosystems in the sediment surrounding the two historic sites, the authors used a remotely operated vehicle to take samples of the sediment at distances from 4 to 60 m along and out from each wreck. The team then extracted and sequenced DNA from any organisms that they collected in the sediment cores to find out what lifeforms were there. Finally, they analysed the differences between the microbial communities at the two shipwreck sites.The team found the greatest microbiome diversity at the site of each shipwreck, decreasing the farther they moved away from it. They also discovered that the shipwrecks have a larger than expected influence on the local microbiology, with distinctive and unique core microbiomes at the two wreck sites. In addition, the presence of the shipwreck changed the availability of nearby tasty elements, such as nitrogen and carbon, that microbes can convert into food for larger organisms. However, the two wrecks affected the seabed in their respective areas in different ways, and the scientists think that this is largely due to differences in shipwreck depth, as well as their proximity to the mouth of the Mississippi river (∼30 km and ∼100 km), washing nutritious material from the land out to sea. Essentially, shipwrecks play a role in supplying deep-sea ecosystems with sustenance to an extent similar to that of other dead material from above, such as whale carcasses.The authors conclude that wooden shipwrecks not only serve to provide refuge and surfaces for organisms to colonise but also are a significant and long-term source of the building blocks upon which diversity can flourish in a setting short of nutrients and far from the shore. Recent surveys of the seafloor in this area of the Gulf of Mexico have identified what appear to be many more nearby shipwrecks with depths in excess of 1000 m that have yet to be surveyed. These unexplored and unidentified sites can undoubtedly tell us more about the ecology of deep-sea microbes and how the arrival of structures made by humans changes the microbial diversity and composition of the seafloor.

Protocolo de tratamiento empírico de la neumonía nosocomial y asociada a ventilador

Hospital-acquired pneumonia (HAP) is a lower respiratory tract infection that is absent at the time of admission which develops after more than 48hours since the hospital admission. Ventilator-associated pneumonia (VAP) is a subgroup of HAP that is very prevalent in intensive care units (ICU). To the extent it is possible, the pertinent microbiological specimens must be collected before starting antimicrobial therapy, but treatment should not be delayed in the event of clinical suspicion. When choosing empirical treatment, we must bear in mind the local microbiology of the hospital and of each hospitalization/intensive care unit, suspicion of multidrug-resistant germs, and severity criteria. The treatment schedules used in the latest national and international guidelines are studied. Currently, indications of seven days of treatment are preferred if clinical progress is favorable.

Clinical factors associated with positive corneal culture in suspected microbial keratitis

AimsDetermine demographic and clinical characteristics associated with positive culture in suspected microbial keratitis. MethodsRetrospective audit of patients that had corneal scrapings between October 1999-September 2004 at Princess Alexandra Hospital. Clinical information was gathered from medical records, smear and culture results from the local microbiology database. Univariate and multivariate analyses of variables associated with positive cultures and calculation of population attributable risk percentage (PAR). ResultsUnivariate analysis showed that positive cultures were associated with patients over 60 years (81% vs 55%; p < 0.001), presenting visual acuity (VA) of 6/24 or worse (74% vs 57%; p = 0.012) or contact lens-related keratitis (CLK 77% vs 62%; p = 0.08). Analysis of patients’ clinical presentation showed that positive culture was associated with a central epithelial defect (74% vs 57%; p = 0.012), anterior chamber reaction of 2 + cells or worse (73% vs 56%; p = 0.03), an epithelial defect of 2 mm or more in diameter (71% vs 50%; p = 0.006) or no prior treatment with antibiotics (68% vs 56%; p = 0.053). Multivariate analysis showed the independent variables associated with positive cultures were VA of 6/24 or worse on presentation, contact lens-related keratitis, age greater than 60 years, an anterior chamber reaction of 2 + cells or worse and no prior treatment with antibiotics. The factor with the highest attributable risk (PAR%) for a positive corneal scraping was VA of 6/24 or worse on presentation (21%). ConclusionsIn this series positive cultures were associated with poor presenting VA contact lens keratitis (CLK), older age, anterior chamber reaction and no prior treatment with antibiotics.

688. Incidence and Risk Factors for Prosthetic Valve Endocarditis Following TAVR: 2015-2019

Abstract Background Transcatheter aortic valve replacement (TAVR) is increasingly used for lower risk patients. Incidence of TAVR endocarditis ranges from 0.2% to 3.3%. The purpose of this study was to determine local incidence and risk factors of prosthetic valve infective endocarditis (PVIE) in a contemporary cohort. Methods IRB approved retrospective, nested case-control study evaluated the 1-year incidence and risk factors for PVIE among TAVR recipients from 2015 to 2019. Inclusion: ≥ 18 years, TAVR procedure at Henry Ford Health System. Exclusion: repeat TAVR. PVIE cases were matched with controls who did not experience PVIE. PVIE defined as diagnosis documentation in the electronic medical record. Figure 1. Study Design Results 23/1266 patients were identified as cases corresponding to a 1-year incidence of 1.82%. The median time to PVIE was 127 days and 35% occurred within 60 days. The most frequently isolated organisms were streptococci (26%), MRSA (13%), and MSSA (13%). Baseline demographics and comorbidities for 23 PVIE cases and 161 controls are displayed in Table 1. Significant risk factors for PVIE in bivariate analysis included STS-PROM (Society of Thoracic Surgeons Predicted Risk of Mortality), median: 4.1 controls and 6.4 cases (p = 0.012). Age, BMI, and comorbidities were not significantly different. Diabetes was notably more frequent among cases (36% vs 48%, p = 0.274). Patients with PVIE had more post-op RBC transfusions (5% vs 21.7% p = 0.003), ECG changes (23% vs 43.5%, p = 0.035), heart block (15.5% vs 34.8%, p = 0.038), longer length of stay (2 days, range 1 to 4 vs 4 to 11, p = 0.004), and thirty-day readmission (10.6% vs 52.2%, p &amp;lt; 0.001). Results displayed in Table 2. Table 1. Patient Characteristics and Risk Factor Analysis Table 2. Additional Outcomes Conclusion The results from this study give insight to the local incidence, microbiology, and risk of PVIE following TAVR. Future directions include a larger evaluation of modifiable risks such as diabetes management and examining the heart block patients who received permanent pacemaker implants. Disclosures Rachel Kenney, PharmD, Medtronic, Inc. (Other Financial or Material Support, spouse is an employee and shareholder) Janet F. Wyman, DNP, CNS-BC, FACC, Edwards Lifesciences (Consultant) Dee Dee Wang, MD, Edwards LifeSciences (Consultant) Brian O'Neill, MD, Edwards Lifesciences (Consultant)

Variation in Bacterial Respiratory Culture Results in Children With Neurologic Impairment.

To examine bacterial respiratory cultures in children with neurologic impairment (NI) (eg, cerebral palsy), both with and without tracheostomies, who were hospitalized with acute respiratory infections (ARIs) (eg, pneumonia) and to compare culture results across hospitals and age groups. This multicenter retrospective cohort study included ARI hospitalizations for children aged 1 to 18 years with NI between 2007 and 2012 who had a bacterial respiratory culture obtained within 2 days of admission. Data from 5 children's hospitals in the Pediatric Health Information System Plus database were used. Organisms consistent with oral flora and nonspeciated organisms were omitted from analysis. The prevalence of positive respiratory culture results and the prevalence of organisms identified were compared across hospitals and age groups and in subanalyses of children with and without tracheostomies by using generalized estimating equations to account for within-patient clustering. Of 4900 hospitalizations, 693 from 485 children had bacterial respiratory cultures obtained. Of these, 54.5% had positive results, although this varied across hospitals (range 18.6%-83.2%; P < .001). Pseudomonas aeruginosa and Staphylococcus aureus were the most commonly identified organisms across hospitals and age groups and in patients with and without tracheostomies. Large variation in growth prevalence was identified across hospitals but not age groups. The bacteriology of ARI in hospitalized children with NI differs from that of otherwise healthy children. Significant variation in prevalence of positive bacterial respiratory culture results and organism growth were observed across hospitals, which may be secondary to local environmental factors and microbiology reporting practices.

INHALE: the impact of using FilmArray Pneumonia Panel molecular diagnostics for hospital-acquired and ventilator-associated pneumonia on antimicrobial stewardship and patient outcomes in UK Critical Care\u2014study protocol for a multicentre randomised controlled trial

BackgroundHospital-acquired and ventilator-associated pneumonias (HAP and VAP) are common in critical care and can be life-threatening. Rapid microbiological diagnostics, linked to an algorithm to translate their results into antibiotic choices, could simultaneously improve patient outcomes and antimicrobial stewardship.MethodsThe INHALE Randomised Controlled Trial is a multi-centre, parallel study exploring the potential of the BioFire FilmArray molecular diagnostic to guide antibiotic treatment of HAP/VAP in intensive care units (ICU); it identifies pathogens and key antibiotic resistance in around 90 min. The comparator is standard care whereby the patient receives empirical antibiotics until microbiological culture results become available, typically after 48–72 h. Adult and paediatric ICU patients are eligible if they are about to receive antibiotics for a suspected lower respiratory infection (including HAP/VAP) for the first time or a change in antibiotic because of a deteriorating clinical condition. Breathing spontaneously or intubated, they must have been hospitalised for 48 h or more. Patients are randomised 1:1 to receive either antibiotics guided by the FilmArray molecular diagnostic and its trial-based prescribing algorithm or standard care, meaning empirical antibiotics based on local policy, adapted subsequently based upon local microbiology culture results. Co-primary outcomes are (i) non-inferiority in clinical cure of pneumonia at 14 days post-randomisation and (ii) superiority in antimicrobial stewardship at 24 h post-randomisation (defined as % of patients on active and proportionate antibiotics). Secondary outcomes include further stewardship reviews; length of ICU stay; co-morbidity indicators, including septic shock, change in sequential organ failure assessment scores, and secondary pneumonias; ventilator-free days; adverse events over 21 days; all-cause mortality; and total antibiotic usage. Both cost-effectiveness of the molecular diagnostic-guided therapy and behavioural aspects determining antibiotic prescribing are being explored. A sample size of 552 will be required to detect clinically significant results with 90% power and 5% significance for the co-primary outcomes.DiscussionThis trial will test whether the potential merits of rapid molecular diagnostics for pathogen and resistance detection in HAP/VAP are realised in patient outcomes and/or improved antibiotic stewardship.Trial registrationISRCTN Registry ISRCTN16483855. Retrospectively registered on 15 July 2019

Improving empiric antibiotic prescribing in pediatric bloodstream infections: a potential application of weighted-incidence syndromic combination antibiograms (WISCA)

ABSTRACT Background: Increasing antibiotic resistance to WHO-recommended first- and second-line treatments of pediatric sepsis requires adaptation of prescribing guidelines. We discuss the potential and limitations of a weighted-incidence syndromic combination antibiogram (WISCA) as a practical tool for incorporating local microbiology data when assessing empiric coverage of commonly used antibiotics. Research design and methods: A brief questionnaire of 18 clinically significant isolates from pediatric blood cultures (Jan-Dec 2018) was sent to a global network of pediatric hospitals in July 2019. Weighted coverage estimates of non-antipseudomonal third-generation cephalosporins (3GC) and meropenem were estimated using Monte–Carlo simulation for each site reporting >100 isolates. Results: 52 hospitals in 23 countries in 5 WHO regions responded to the questionnaire; 13 sites met the sample size requirement. The most common isolates were S. aureus, Klebsiella spp., E. coli and Enterococcus spp. Coverage of 3GC ranged from 39% [95%CrI: 34–43%] to 73% (two sites: [95%CrI: 65–80%]; [95%CrI: 68–86%]) and meropenem coverage ranged from 54% [95%CrI: 47–60%] to 88% [95%CrI:84–91%]. Conclusions: A WISCA is a data-driven, clinically intuitive tool that can be used to compare empiric antibiotic regimens for pediatric sepsis using existing large datasets. The estimates can be further refined using more complex meta-analytical methods and patient characteristics.

P-62 INFECTIONS IN THE FIRST MONTH POST LIVER TRANSPLANTATION IN A TRANSPLANT CENTER IN CHILE

Infections are an important cause of morbidity and mortality in the first month after liver transplantation (LT). It is important to know the local microbiology involved and the resistance patterns, to guide treatment appropriately. To characterize infections in the first month after LT in patients from the Hospital Clínico de la Universidad de Chile. Retrospective study of clinical records of 70 consecutive LT between February 2016 and October 2018. 20 infectious events in 16 patients (23%). In 75% it was possible to isolate agent. Eight (40%) were bacteria, 5 were fungi and 2 were viruses; 25% were bacteremia, 20% urinary tract, 20% pulmonary, 10% intra-abdominal, and 5% skin. The agents were: K. pneumoniae (2), S. epidermidis (2), E. faecium (1), C. freundii (1), E. coli (1), S. malthophilia (1). Candidas (4), Aspergillus (1), varicella zoster virus (1), respiratory syncytial virus (1). It was not possible to identify a focus in 4 patients. There was antimicrobial resistance in 7 (35%) of the cases, 3 being multi-resistant (2 due to K. pneumoniae and 1 due to S. epidermidis). 4 microorganisms showed antimicrobial resistance (E. coli, C. freundii, E. faecium, and C. glabatra). The infection was the cause of in-hospital mortality in 2 patients. Infections in the first month after LT are frequent in our center, the majority of bacterial origin, as reported by international series. More than 1/3 of the patients present an agent with antimicrobial resistance, which should be considered in the choice of empirical therapy.

Microbiological profile and antibiotic resistance pattern of empyema thoracis in Calabar, Nigeria.

Targeted empirical antibiotic therapy based on local microbiology and antibiotic resistance patterns is essential for the treatment of empyema thoracis. Our retrospective review of 105 pleural empyema culture and sensitivity reports aimed at determining the causative microorganisms and their antimicrobial resistance pattern. Of 105 pleural aspirate samples, 46 (43.8%) were positive on culture. Gram-negative organisms (n = 43) were the predominant isolates, the commonest of which was Klebsiella pneumoniae. It was concluded that empyema thoracis is predominantly caused by Gram-negative organisms in our locality. This should guide protocols on the initiation of empirical therapy.

Incidence of Infection during the First Year after Lung Transplant in a Colombian Center between 2007 and 2019

Purpose Infections are of great concern in lung transplant recipients due to multiple factors. Few studies have evaluated its prevalence and etiology in these patients. Our objective was to characterize infections in the first year after transplant, emphasizing on healthcare-associated infections (HAI), in a program in Colombia Methods Descriptive, retrospective and longitudinal study. We included lung transplant recipients between 2007-2019 in a Colombian institution. Variables were taken from patient's medical records. Analysis was made in SPSS v21®. Results 85 patients were included. 5 (5.9%) patients were excluded due to perioperative demise and 4 (4.7%) due to incomplete medical record. 52.6% (n=40) were male, median age at transplant was 51 (IQR 38-59), and COPD (40.8%) was the main transplant reason. 96% and 92% of the patients received prophylaxis against CMV and fungi, respectively; and 91% received post-transplant trimethoprim sulfamethoxazole. 185 infections were reported in 65 (85.5%) patients in the first year, and pneumonia was the leading infection, causing 40.5% of cases (n=75). Infections distribution was 35.7%, 42.2% and 22.2% in months 1, 2 to 6 and 7 to 12, respectively; and etiology varied between bacterial (35.7%), fungal (15.1%), viral (9.7%), and parasitic (1.6%). Most isolated microorganisms were P. aeruginosa (8.7%), citomegalovirus (6.5%), Candida spp. (6.5%), K. pneumoniae (5.9%) and Aspergillus spp. (5.4%). 15 infections (8.1%) were polymicrobial, and there was no microbial isolation in 55 cases (29.7%). 60 HAI were reported in 30 patients in the first year, 16.6% were polymicrobial and no microorganism was found in 10%. 70% of HAI (n=42) took place in ICU, and 23 were attributable to invasive devices. 13 (21.6%) HAI happened in general ward inpatients, where pneumonia was the most frequent infection (21.6%). 5 HAI were due to surgical site infection (8.6%). Between 2015 and 2019 HAI decreased 50% compared to 2009-2014. 25/76 patients died (32.8%), and infection-attributable mortality was 68%. Conclusion Infections impact lung transplant outcomes significantly in our setting. Institutional protocols must be adjusted according to local microbiology and infection prevalence, emphasizing on healthcare-associated infections.

Association of Local Unit Sampling and Microbiology Laboratory Culture Practices With the Ability to Identify Causative Pathogens in Peritoneal Dialysis-Associated Peritonitis in Thailand

IntroductionThis describes variations in facility peritoneal dialysis (PD) effluent (PDE) culture techniques and local microbiology laboratory practices, competencies, and quality assurance associated with peritonitis, with a specific emphasis on factors associated with culture-negative peritonitis (CNP).MethodsPeritonitis data were prospectively collected from 22 Thai PD centers between May 2016 and October 2017 as part of the Peritoneal Dialysis Outcomes and Practice Patterns Study. The first cloudy PD bags from PD participants with suspected peritonitis were sent to local and central laboratories for comparison of pathogen identification. The associations between these characteristics and CNP were evaluated.ResultsCNP was significantly more frequent in local laboratories (38%) compared with paired PDE samples sent to the central laboratory (12%, P < 0.05). Marked variations were observed in PD center practices, particularly with respect to specimen collection and processing, which often deviated from International Society for Peritoneal Dialysis Guideline recommendations, and laboratory capacities, capabilities, and certification. Lower rates of CNP were associated with PD nurse specimen collection, centrifugation of PDE, immediate transfer of samples to the laboratory, larger hospital size, larger PD unit size, availability of an on-site nephrologist, higher laboratory capacity, and laboratory ability to perform aerobic cultures, undertake standard operating procedures in antimicrobial susceptibilities, and obtain local accreditation.ConclusionThere were large variations in PD center and laboratory capacities, capabilities, and practices, which in turn were associated with the likelihood of culturing and correctly identifying organisms responsible for causing PD-associated peritonitis. Deviations in practice from International Society for Peritoneal Dialysis guideline recommendations were associated with higher CNP rates.

A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing

Whole-genome sequencing is likely to become increasingly used by local clinical microbiology laboratories, where sequencing volume is low compared with national reference laboratories. Here, we describe a universal protocol for simultaneous DNA extraction and sequencing of numerous different bacterial species, allowing mixed species sequence runs to meet variable laboratory demand. We assembled test panels representing 20 clinically relevant bacterial species. The DNA extraction process used the QIAamp mini DNA kit, to which different combinations of reagents were added. Thereafter, a common protocol was used for library preparation and sequencing. The addition of lysostaphin, lysozyme or buffer ATL (a tissue lysis buffer) alone did not produce sufficient DNA for library preparation across the species tested. By contrast, lysozyme plus lysostaphin produced sufficient DNA across all 20 species. DNA from 15 of 20 species could be extracted from a 24-h culture plate, while the remainder required 48–72 h. The process demonstrated 100% reproducibility. Sequencing of the resulting DNA was used to recapitulate previous findings for species, outbreak detection, antimicrobial resistance gene detection and capsular type. This single protocol for simultaneous processing and sequencing of multiple bacterial species supports low volume and rapid turnaround time by local clinical microbiology laboratories.

647. Adoption of the updated fluoroquinolones breakpoints for Gram negative bacteria in clinical microbiology laboratories

BackgroundDespite the multiple safety warnings related to fluoroquinolones (FQs) treatment, their use remains unavoidable in several occasions due to their broad spectrum of coverage including activity against multi-drug resistant glucose non-fermenting Gram-negative bacteria such as Pseudomonas spp., and high oral bioavailability. The Clinical and Laboratory Standards Institute (CLSI) has lowered the FQs minimal inhibitory concentrations (MICs) breakpoints for Salmonella spp. in 2012 and 2013, and for the Enterobacterales and P. aeruginosa in 2019. We aim to explore the number of hospitals that adopted the revised breakpoints.MethodsWe conducted a cross-sectional phone-based survey querying the 43 microbiology laboratories that serve 100% of the acute care and long-term hospitals in Connecticut to determine use of revised FQs MIC breakpoints for Gram-negative bacteria.ResultsSix laboratories refer antimicrobial susceptibility testing to another local hospital microbiology laboratory or to a national reference laboratory. Thus, we obtained information about the study question from a total of 37 microbiology laboratories. Eight laboratories (21.6%) were affiliated to university hospitals and 29 (78.4%) were community-based. Microscan Beckman coulter MicroScan was the most common antimicrobial susceptibility test method used in 15 (40.6%) microbiology laboratories followed by BioMérieux Vitek 2 in 13 (35.1%) laboratories. Four laboratories (10.8%) only adopted the revised CLSI FQs breakpoints for Enterobacterales, P. aeruginosa, and Salmonella spp, 5 (13.5%) implemented the revised breakpoints for Enterobacterales and P. aeruginosa but not for Salmonella spp., and 8 (21.6%) laboratories adopted the revised CLSI breakpoints for Salmonella spp. but not for Enterobacterales and P. aeruginosa.ConclusionThe use of outdated CLSI breakpoints for FQs against Gram-negative bacteria remains common in the microbiology laboratories. There is an urgent need to mitigate the impact of using the outdated FQs breakpoints and reporting false susceptibility to FQs.Disclosures All Authors: No reported disclosures

158. A multi-site, prospective study of antimicrobial prescribing practices in three low- or middle-income country hospitals

BackgroundAntimicrobial stewardship programs (ASPs) are being developed internationally to mitigate the misuse of antimicrobials. An understanding of current practices and prescribing patterns is necessary to determine targets to develop context-specific ASPs in low- and middle-income country (LMIC) hospitals.MethodsWe conducted a prospective study of patients admitted to the adult medical wards at three LMIC tertiary care centers in 2018- 2019: a 1,800-bed public hospital in Galle, Sri Lanka; a 991-bed public hospital in Eldoret, Kenya; and a 630-bed private hospital in Moshi, Tanzania. Information regarding antimicrobial therapy received during hospitalization, indications for antimicrobial therapy, and duration of antimicrobial use were extracted from the medical record.ResultsIn total, 3150 patients were enrolled: 1297 in Sri Lanka, 750 in Kenya, and 1103 in Tanzania. Antimicrobial use prevalence varied between the three sites, with 56.0% of patients receiving antimicrobials during hospitalization in Sri Lanka, 56.5% in Kenya, and 35.4% in Tanzania. Third-generation cephalosporins were used most frequently in Kenya (70.0%) and Tanzania (73.1%), whereas amoxicillin/ clavulanic acid was used most frequently in Sri Lanka (48.4%). Lower respiratory tract infection was the most common indication for antimicrobial use in all three locations: 37.4% in Sri Lanka, 27.8% in Kenya, and 49.2% in Tanzania. No clear indication for antimicrobial use was documented among 11.6% patients receiving antimicrobials in Sri Lanka, 32.8% in Kenya, and 10.5% in Tanzania. In Tanzania, 8.6% of the patients had documentation of input from the microbiology or infectious diseases teams compared to less than 1% in either Sri Lanka or Kenya. Pertinent culture data related to the primary indication for antimicrobials was present in 16.1% (Sri Lanka), 6.1% (Kenya), and 7.4% (Tanzania).ConclusionUnclear documentation for antimicrobial use was common in all three sites and most patients on antimicrobial therapy did not have pertinent culture data. Improving documentation and the capacity of the local microbiology laboratories could be initial targets for ASPs in these LMIC hospitals.Disclosures All Authors: No reported disclosures

Diabetic Foot Infections: Bacterial Isolates From the Centers and Hospitals of Latin American Countries.

Diabetic foot infections (DFIs) are one of the most important reasons for lower limb amputations. An adequate approach to the management of DFI implies control of infection using strategies of tissue debridement and empirical antibiotic treatment based on local microbiology. The aim of this study was to determine the bacterial isolates profile and antibiotic susceptibility patterns in samples from DFI from Latin American centers, on the premise that microbiology of this region differs from that of other continents and influences antimicrobial election. Three hundred and eighty-two samples from soft tissue and bone were studied from 17 centers of 4 countries. Three hundred and seven (80.4%; 95% confidence interval = 75.9-84.2) were positive. Gram negatives (GN) were isolated in 43.8% of all samples, not only in severe but also in mild infections, 51% in bone samples, more frequently in presence of ischemia (47% vs 38%; P = .07) and in wounds with longer duration of the lesion (30-20 days; P < .01). Staphylococcus aureus was the most frequent single germ (19.9%). Gram positives were isolated more frequently in patients without ischemia (53% vs 40%; P = .01). Enterococcus faecalis was the most frequent germ in bone samples (16.8%). Ciprofloxacin and trimethoprim-sulfamethoxazole were the oral antimicrobials most effective against GN. Trimethoprim-sulfamethoxazole and rifampicin were the oral antimicrobials most effective against Staphylococcus. Because of GN high antibiotic resistance patterns, patients treated in an ambulatory setting have to be controlled early after starting empiric treatment to assess response to therapy and hospitalize for parenteral antibiotics if oral treatment fails.

Expanding antimicrobial stewardship strategies for the NICU: Management of surgical site infections, perioperative prophylaxis, and culture negative sepsis

Objective: To review antibiotic stewardship strategies for neonatal intensive care units (NICU) in the areas of management of surgical site infections, perioperative prophylaxis and culture negative late onset sepsis. Finding: Review of local microbiology, stratification of surgical procedures by risk of contamination of the surgical site, and adherence to evidence-based principles of perioperative antibiotic administration (targeted therapy, effective dosing, appropriate timing and limiting duration post-operatively) can help to minimize unnecessary antibiotic use for neonatal surgery. Creating a late onset sepsis case definition, appropriate collection and interpretation of blood cultures, and instituting antibiotic time-outs can minimize the overuse of antibiotics for culture negative sepsis. Conclusion: Effective implementation of these antimicrobial stewardship strategies in the NICU can reduce unnecessary antimicrobial use and limit the emergence of resistant pathogens.

Antimicrobial susceptibility of isolated pathogens from patients with contact lens-related bacterial keratitis in Crete, Greece: A ten-year analysis

PurposeTo evaluate the bacterial spectrum and antimicrobial susceptibilities of pathogens isolated from contact lens-related bacterial keratitis cases in a large academic Greek hospital. MethodsAll adult patients with positive corneal scrapings or contact lens culture between 2007 and 2016 at the University Hospital of Heraklion, Greece, were retrospectively identified through a local microbiology database and their medical records were reviewed. ResultsA total of 240 isolates were recovered from 131 patients with culture-proven contact lens-associated bacterial keratitis. The most common microorganism identified was Serratia marcescens (17.1% of total isolates), followed by Pseudomonas aeruginosa, Klebsiella spp. and coagulase-negative staphylococci (CoNS). Rates of aztreonam-resistant P. aeruginosa and erythromycin-resistant CoNS decreased in recent years, while the decrease in oxacillin-resistant CoNS was statistically significant (p=0.009). More than 90% of the isolated organisms (S. marcescens, P. aeruginosa, Klebsiella spp. and CoNS) were susceptible to ciprofloxacin or gentamicin. ConclusionGram-negative microorganisms are the most common causative pathogens of contact lens-related keratitis in the region of Crete. Topical antibacterials containing quinolones or gentamicin represent an effective empirical treatment for the majority of the cases. This is quite encouraging, considering that the present study was conducted in a country characterised by high antimicrobial resistance rates. However, culture-driven antimicrobial treatment is mandatory for this sight-threatening infection.

On giant shoulders: how a seamount affects the microbial community composition of seawater and sponges

Abstract. Seamounts represent ideal systems to study the influence and interdependency of environmental gradients at a single geographic location. These topographic features represent a prominent habitat for various forms of life, including microbiota and macrobiota, spanning benthic as well as pelagic organisms. While it is known that seamounts are globally abundant structures, it still remains unclear how and to which extent the complexity of the sea floor is intertwined with the local oceanographic mosaic, biogeochemistry, and microbiology of a seamount ecosystem. Along these lines, the present study aimed to explore whether and to what extent seamounts can have an imprint on the microbial community composition of seawater and of sessile benthic invertebrates, sponges. For our high-resolution sampling approach of microbial diversity (16S rRNA gene amplicon sequencing) along with measurements of inorganic nutrients and other biogeochemical parameters, we focused on the Schulz Bank seamount ecosystem, a sponge ground ecosystem which is located on the Arctic Mid-Ocean Ridge. Seawater samples were collected at two sampling depths (mid-water, MW, and near-bed water, BW) from a total of 19 sampling sites. With a clustering approach we defined microbial microhabitats within the pelagic realm at Schulz Bank, which were mapped onto the seamount's topography and related to various environmental parameters (such as suspended particulate matter, SPM; dissolved inorganic carbon, DIC; silicate, SiO4-; phosphate, PO43-; ammonia, NH4+; nitrate, NO32-; nitrite, NO2-; depth; and dissolved oxygen, O2). The results of our study reveal a “seamount effect” (sensu stricto) on the microbial mid-water pelagic community at least 200 m above the sea floor. Further, we observed a strong spatial heterogeneity in the pelagic microbial landscape across the seamount, with planktonic microbial communities reflecting oscillatory and circulatory water movements, as well as processes of bentho-pelagic coupling. Depth, NO32-, SiO4-, and O2 concentrations differed significantly between the determined pelagic microbial clusters close to the sea floor (BW), suggesting that these parameters were presumably linked to changes in microbial community structures. Secondly, we assessed the associated microbial community compositions of three sponge species along a depth gradient of the seamount. While sponge-associated microbial communities were found to be mainly species-specific, we also detected significant intra-specific differences between individuals, depending on the pelagic near-bed cluster they originated from. The variable microbial phyla (i.e. phyla which showed significant differences across varying depth, NO32-, SiO4-, O2 concentrations, and different from local seawater communities) were distinct for every sponge species when considering average abundances per species. Variable microbial phyla included representatives of both those taxa traditionally counted for the variable community fraction and taxa counted traditionally for the core community fraction. Microbial co-occurrence patterns for the three examined sponge species Geodia hentscheli, Lissodendoryx complicata, and Schaudinnia rosea were distinct from each other. Over all, this study shows that topographic structures such as the Schulz Bank seamount can have an imprint (seamount effect sensu lato) on both the microbial community composition of seawater and sessile benthic invertebrates such as sponges by an interplay between the geology, physical oceanography, biogeochemistry, and microbiology of seamounts.

Epidemiology of carbapenemase-producing Enterobacterales in England, May 2015–March 2019: national enhanced surveillance findings and approach

In response to increasing numbers of carbapenemase-producing Enterobacterales (CPE) in England, Public Health England (PHE) launched an electronic reporting system (ERS) for the enhanced surveillance of carbapenemase-producing Gram-negative bacteria. Our study aimed to describe system engagement and the epidemiology of CPE in England. Engagement with the ERS was assessed by calculating the proportion of referrals submitted this system. ERS data were extracted and cases defined as patients with CPE isolated from a screening or clinical specimen in England between 1st May 2015 to 31st March 2019. Descriptive summary statistics for each variable were prepared. The ERS processed 12,656 suspected CPE reports. Uptake of the ERS by local microbiology laboratories varied, with approximately 70% of referrals made via the ERS by April 2016; this steadily decreased after March 2018. Six-thousand eight-hundred and fifty-seven cases were included in the analysis. Most cases were from colonised patients (80.6%) rather than infected, and the majority were inpatients in acute hospital settings (87.3%). Carbapenemases were most frequently detected in Klebsiella pneumoniae (39.1%) and Escherichia coli (30.3%). The most frequently identified carbapenemase families were OXA-48-like (45.1%) and KPC (26.4%). Enhanced data variables were poorly completed. The ERS has provided some insight into the epidemiology of CPE in England. An increasing number of routine diagnostic laboratories have introduced methods to routinely identify acquired carbapenemases and PHE has modified its approach to ensure robust surveillance, which is an essential aspect of an effective response to prevent and control the spread of CPE.

HALLAZGOS MICROBIOLÓGICOS Y SUSCEPTIBILIDAD ANTIMICROBIANA EN CIRUGÍA ABDOMINAL DE URGENCIA.

Introducción: Es importante mantener programas de vigilancia bacteriana para disminuir resistencia y definir esquemas farmacológicos adecuados. Los pacientes con abdomen agudo representan un grupo microbiológico especial.Objetivos: Hacer una revisión de agentes patógenos en pacientes adultos operados en nuestro Servicio de Urgencia por patología abdominal con líquido libre y analizar los resultados obtenidos de cultivos respecto a las cepas y la suceptibilidad a los antibióticos. Materiales y Método: Estudio de cohorte prospectiva con estadística descriptiva. Se incluyen pacientes consecutivos, mayores de 18 años, operados por abdomen agudo que presentan liquido libre intraperitoneal entre noviembre de 2017 y abril de 2018.Se excluyen casos con terapia antimicrobiana, hospitalización y/o cirugía en los 3 meses previos. Se registran los cultivos positivos, cepas aisladas, susceptibilidad antimicrobiana, datos demográficos y evolución clínica.Resultados: De 63 pacientes 55% fueron hombres y la edad promedio 52,2 años. Las patologías más frecuentes fueron de origen apendicular (62%) y de causa entérica (30%). En un 44% el cultivo fue positivo y en 36% con más de un germen. Escherichia coli fue el patógeno más frecuente (64,2%) seguidos de Enterococo faecium y Estreptococo anginosus (7,1%). De los otros patógenos cultivados sólo se observó resistencia múltiple en un caso aislado de Morganella Morganii.Conclusiones: Estos datos constituyen la realidad microbiológica local en abdomen agudo. La Escherichia Coli sigue siendo el germen más frecuente, debe enfrentarse con profilaxis y tratamiento antibiótico adecuado. Es necesario mantener vigilancia microbiología local para un manejo acorde.