The COVID-19 Pandemic Sparked off a Large-Scale Outbreak of Carbapenem-Resistant Acinetobacter baumannii from the Endemic Strains at an Italian Hospital

Acinetobacter baumannii is a nosocomial pathogen that poses a serious threat due to the rise of incidence of multidrug-resistant (MDR) strains. During the COVID-19 pandemic, MDR A. baumannii clones have caused several outbreaks worldwide. Here, we describe a detailed investigation of an MDR A. baumannii outbreak that occurred at Policlinico San Matteo (Pavia, Italy). A total of 96 A. baumannii strains, isolated between January and July 2020 from 41 inpatients (both SARS-CoV-2 positive and negative) in different wards, were characterized by phenotypic and genomic analyses combining Illumina and Nanopore sequencing. Antibiotic susceptibility testing revealed that all isolates were resistant to carbapenems, and the sequence analysis attributed this to the carbapenemase gene blaOXA-23. Virulence factor screening unveiled that all strains carried determinants for biofilm formation, while plasmid analysis revealed the presence of two plasmids, one of which was ~100 kbp long and encoded a phage sequence. A core genome-based phylogeny was inferred to integrate outbreak strain genomes with background genomes from public databases and the local surveillance program. All strains belonged to the globally disseminated sequence type 2 (ST2) clone and were mainly divided into two clades. Isolates from the outbreak clustered with surveillance isolates from 2019, suggesting that the outbreak was caused by two strains that were already circulating in the hospital before the start of the pandemic. The intensive spread of A. baumannii in the hospital was enhanced by the extreme emergency situation of the first COVID-19 pandemic wave that resulted in reduced attention to infection prevention and control practices. IMPORTANCE: The COVID-19 pandemic, especially during the first wave, posed a great challenge to the hospital management and generally promoted nosocomial pathogen dissemination. MDR A. baumannii can easily spread and persist for a long time on surfaces, causing outbreaks in health care settings. Infection prevention and control practices, epidemiological surveillance, and microbiological screening are fundamental in order to control such outbreaks. Here, we sequenced the genomes of 96 isolates from an outbreak of MDR A. baumannii strains using both short- and long-read technology in order to reconstruct the outbreak events in fine detail. The sequence data demonstrated that two endemic clones of MDR A. baumannii were the source of this large hospital outbreak during the first COVID-19 pandemic wave, confirming the effect of COVID-19 emergency disrupting the protection provided by the use of the standard prevention procedures

Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae

During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50=615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage= 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and "Superficieibacter." An ortholog-based phylogenomic analysis indicated a sister group relationship with "Superficieibacter electus," in a distinct Glade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of "Superficiebacter," average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus "Superficieibacter." We propose for the new species the name "Superficieibacter maynardsmithii."Peer reviewe

Pre-hospital plasma in haemorrhagic shock management: current opinion and meta-analysis of randomized trials

Abstract Background Trauma-induced coagulopathy is one of the most difficult issues to manage in severely injured patients. The plasma efficacy in treating haemorrhagic-shocked patients is well known. The debated issue is the timing at which it should be administered. Few evidences exist regarding the effects on mortality consequent to the use of plasma alone given in pre-hospital setting. Recently, two randomized trials reported interesting and discordant results. The present paper aims to analyse data from those two randomized trials in order to obtain more univocal results. Methods A systematic review with meta-analysis of randomized controlled trials (RCTs) of pre-hospital plasma vs. usual care in patients with haemorrhagic shock. Results Two high-quality RCTs have been included with 626 patients (295 in plasma and 331 in usual care arm). Twenty-four-hour mortality seems to be reduced in pre-hospital plasma group (RR = 0.69; 95% CI = 0.48–0.99). Pre-hospital plasma has no significant effect on 1-month mortality (RR = 0.86; 95% CI = 0.68–1.11) as on acute lung injury and on multi-organ failure rates (OR = 1.03; 95% CI = 0.71–1.50, and OR = 1.30; 95% CI = 0.92–1.86, respectively). Conclusions Pre-hospital plasma infusion seems to reduce 24-h mortality in haemorrhagic shock patients. It does not seem to influence 1-month mortality, acute lung injury and multi-organ failure rates. Level of evidence: Level I Study type: Systematic review with Meta-analysi

Implications of ICU triage decisions on patient mortality: a cost-effectiveness analysis

INTRODUCTION: Intensive care is generally regarded as expensive, and as a result beds are limited. This has raised serious questions about rationing when there are insufficient beds for all those referred. However, the evidence for the cost effectiveness of intensive care is weak and the work that does exist usually assumes that those who are not admitted do not survive, which is not always the case. Randomised studies of the effectiveness of intensive care are difficult to justify on ethical grounds; therefore, this observational study examined the cost effectiveness of ICU admission by comparing patients who were accepted into ICU after ICU triage to those who were not accepted, while attempting to adjust such comparison for confounding factors. METHODS: This multi-centre observational cohort study involved 11 hospitals in 7 EU countries and was designed to assess the cost effectiveness of admission to intensive care after ICU triage. A total of 7,659 consecutive patients referred to the intensive care unit (ICU) were divided into those accepted for admission and those not accepted. The two groups were compared in terms of cost and mortality using multilevel regression models to account for differences across centres, and after adjusting for age, Karnofsky score and indication for ICU admission. The analyses were also stratified by categories of Simplified Acute Physiology Score (SAPS) II predicted mortality (40%). Cost effectiveness was evaluated as cost per life saved and cost per life-year saved. RESULTS: Admission to ICU produced a relative reduction in mortality risk, expressed as odds ratio, of 0.70 (0.52 to 0.94) at 28 days. When stratified by predicted mortality, the odds ratio was 1.49 (0.79 to 2.81), 0.7 (0.51 to 0.97) and 0.55 (0.37 to 0.83) for 40% predicted mortality, respectively. Average cost per life saved for all patients was $103,771 (€82,358) and cost per life-year saved was$7,065 (€5,607). These figures decreased substantially for patients with predicted mortality higher than 40%, $60,046 (€47,656) and$4,088 (€3,244), respectively. Results were very similar when considering three-month mortality. Sensitivity analyses performed to assess the robustness of the results provided findings similar to the main analyses. CONCLUSIONS: Not only does ICU appear to produce an improvement in survival, but the cost per life saved falls for patients with greater severity of illness. This suggests that intensive care is similarly cost effective to other therapies that are generally regarded as essential

A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings

Genomic analyses of Klebsiella isolates sampled from multiple human, animal and environmental sources in Northern Italy explore Klebsiella population diversity and show that transmission of multidrug-resistant clones between clinical and environmental settings is scarce.The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 17-month period from a wide range of clinical, community, animal and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired carbapenem non-susceptible Klebsiella and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.Peer reviewe

Genome of Superficieibacter maynardsmithii, a novel, antibiotic susceptible representative of Enterobacteriaceae

During a citywide microbiological screening project in Pavia (Italy) a bacterial strain isolated from the surface of an Automated Teller Machine was classified as a Klebsiella sp. by MALDI-TOF spectrometry, and shown to be susceptible to the most antimicrobial classes by phenotypic testing. After Illumina genome sequencing and subsequent assembly, a high-quality draft genome was obtained (size = 5,051,593 bp, N50 = 615,571 bp, largest contig = 1,328,029 bp, N_contig = 17, GC content = 51.58%, coverage = 141.42), absence of antimicrobial resistance genes was confirmed, but the strain resulted to be highly divergent from all Klebsiella, and more related to other Enterobacteriaceae. The higher values of 16S rRNA identity were with members of the genera Citrobacter, Salmonella, and “Superficieibacter.” An ortholog-based phylogenomic analysis indicated a sister group relationship with “Superficieibacter electus,” in a distinct clade from other members of the Enterobacteriaceae family. In order to evaluate whether the novel genome represents a new species of “Superficiebacter,” average nucleotide identity (ANI) and Hadamard analysis were performed on a dataset of 78 Enterobacteriaceae. The novel genome showed an ANI of 87.51% with S. electus, which compared on identity values between other members of the family, clearly indicates that the genome represents a new species within the genus “Superficieibacter.” We propose for the new species the name “Superficieibacter maynardsmithii.”</p

Description of Klebsiella spallanzanii sp. nov. and of Klebsiella pasteurii sp. nov.

Klebsiella oxytoca causes opportunistic human infections and post-antibiotic haemorrhagic diarrhea. This Enterobacteriaceae species is genetically heterogeneous and is currently subdivided into seven phylogroups (Ko1 to Ko4 and Ko6 to Ko8). Here we investigated the taxonomic status of phylogroups Ko3 and Ko4. Genomic sequence-based phylogenetic analyses demonstrate that Ko3 and Ko4 formed well-defined sequence clusters related to, but distinct from, Klebsiella michiganensis (Ko1), K. oxytoca (Ko2), K. huaxiensis (Ko8), and K. grimontii (Ko6). The average nucleotide identity (ANI) of Ko3 and Ko4 were 90.7% with K. huaxiensis and 95.5% with K. grimontii, respectively. In addition, three strains of K. huaxiensis, a species so far described based on a single strain from a urinary tract infection patient in China, were isolated from cattle and human feces. Biochemical and MALDI-ToF mass spectrometry analysis allowed differentiating Ko3, Ko4, and Ko8 from the other K. oxytoca species. Based on these results, we propose the names Klebsiella spallanzanii for the Ko3 phylogroup, with SPARK_775_C1T (CIP 111695T and DSM 109531T) as type strain, and Klebsiella pasteurii for Ko4, with SPARK_836_C1T (CIP 111696T and DSM 109530T) as type strain. Strains of K. spallanzanii were isolated from human urine, cow feces, and farm surfaces, while strains of K. pasteurii were found in fecal carriage from humans, cows, and turtles.Peer reviewe

Intraoperative surgical site infection control and prevention : a position paper and future addendum to WSES intra-abdominal infections guidelines

Correction: Volume: 16 Issue: 1, Article Number: 18 DOI: 10.1186/s13017-021-00361-4Background Surgical site infections (SSI) represent a considerable burden for healthcare systems. They are largely preventable and multiple interventions have been proposed over past years in an attempt to prevent SSI. We aim to provide a position paper on Operative Room (OR) prevention of SSI in patients presenting with intra-abdominal infection to be considered a future addendum to the well-known World Society of Emergency Surgery (WSES) Guidelines on the management of intra-abdominal infections. Methods The literature was searched for focused publications on SSI until March 2019. Critical analysis and grading of the literature has been performed by a working group of experts; the literature review and the statements were evaluated by a Steering Committee of the WSES. Results Wound protectors and antibacterial sutures seem to have effective roles to prevent SSI in intra-abdominal infections. The application of negative-pressure wound therapy in preventing SSI can be useful in reducing postoperative wound complications. It is important to pursue normothermia with the available resources in the intraoperative period to decrease SSI rate. The optimal knowledge of the pharmacokinetic/pharmacodynamic characteristics of antibiotics helps to decide when additional intraoperative antibiotic doses should be administered in patients with intra-abdominal infections undergoing emergency surgery to prevent SSI. Conclusions The current position paper offers an extensive overview of the available evidence regarding surgical site infection control and prevention in patients having intra-abdominal infections.Peer reviewe

COVID-19 the showdown for mass casualty preparedness and management: the Cassandra Syndrome.

Since December 2019, the world is potentially facing one of the most difficult infectious situations of the last decades. COVID-19 epidemic warrants consideration as a mass casualty incident (MCI) of the highest nature. An optimal MCI/disaster management should consider all four phases of the so-called disaster cycle: mitigation, planning, response, and recovery. COVID-19 outbreak has demonstrated the worldwide unpreparedness to face a global MCI.This present paper thus represents a call for action to solicitate governments and the Global Community to actively start effective plans to promote and improve MCI management preparedness in general, and with an obvious current focus on COVID-19

COVID-19 the showdown for mass casualty preparedness and management: the Cassandra Syndrome.

Since December 2019, the world is potentially facing one of the most difficult infectious situations of the last decades. COVID-19 epidemic warrants consideration as a mass casualty incident (MCI) of the highest nature. An optimal MCI/disaster management should consider all four phases of the so-called disaster cycle: mitigation, planning, response, and recovery. COVID-19 outbreak has demonstrated the worldwide unpreparedness to face a global MCI.This present paper thus represents a call for action to solicitate governments and the Global Community to actively start effective plans to promote and improve MCI management preparedness in general, and with an obvious current focus on COVID-19