The ATCC genome portal: 3,938 authenticated microbial reference genomes.

The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC's biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO 9000 by ATCC. Here, we present new features and content added to the AGP for the research community.

Robotic Surgery for Pediatric Choledochal Cysts: An American Case Series and Literature Review.

INTRODUCTION: Choledochal cysts are rare congenital biliary cystic dilations. The US incidence rate varies between 5 and 15 cases per 1,000,000 people. In contrast, Asians, which are a large subset of the population of Hawaii, have an incidence of approximately one in every 1000 births. We report our experience with robot-assisted laparoscopic surgical management with biliary reconstruction of choledochal cysts which to date is the largest American case series to be reported. MATERIALS AND METHODS: From 2006 to 2021, patients diagnosed with a choledochal cyst(s) at a tertiary children's hospital were retrospectively reviewed. Perioperative analysis was performed. Complications were defined as immediate, early, or late. The data underwent simple descriptive statistics. RESULTS: Nineteen patients underwent choledochal cystectomy and hepaticoduodenostomy. Thirteen underwent a robotic approach while the rest were planned laparoscopic. Eighteen of 19 were female with 15/19 of Asian descent. The ages ranged from 5 mo to 21 y. Presenting diagnoses included jaundice, primary abdominal pain, pancreatitis, and cholangitis. Sixty eight percent had type 1 fusiform cysts while the rest were type 4a. Operative time and length of stay for robotic versus laparoscopic were 321 versus 267 min and 8.2 versus 17.3 d, respectively. For the robotic group, there was one immediate complication due to peritonitis. One-year follow-up revealed two patients requiring endoscopic retrograde cholangiopancreatography with dilation/stenting for an anastomotic stricture. There were no anastomotic leaks. CONCLUSIONS: Robot-assisted laparoscopic choledochal cystectomy with hepaticoduodenostomy is associated with overall good outcomes with the most common long-term complication being anastomotic stenosis.

Terrisporobacter hibernicus sp. nov., isolated from bovine faeces in Northern Ireland.

A new species of Terrisporobacter, a Gram-positive, spore-forming anaerobic group, proposed name Terrisporobacter hibernicus sp. nov., was isolated in Northern Ireland from bovine faeces collected in 2016. Designated as MCA3T, cells of T. hibernicus sp. nov. are rod shaped and motile. Cells tolerate NaCl from 0.5 to 5.5 % (w/v), with a pH tolerance between pH 6 and 9. The optimal temperature for growth is 35-40 °C, and temperatures from 20 to 30 °C are tolerated. The polar lipid profile displays diphosphatidylglycerol, phosphatidylglycerol, two aminoglycolipids, one glycophospholipid, one aminolipid, three glycolipids, five phospholipids and one lipid. No respiratory quinones are detected. The predominant fatty acid profile includes C16 : 0 at 22.8 %. Strain MCA3T is positive for glucose and maltose acidification, as well as glycerol and sorbitol. The biochemical results from a VITEK2 assay of strain MCA3T, Terrisporobacter petrolearius LAM0A37T and Terrisporobacter mayombei DSM 6539T are also included for the first time. The closed and complete genome of strain MCA3T from a hybrid Oxford Nanopore Technology MinION/Illumina assembly reveals no evidence for known virulence genes. Draft genome sequencing of T. mayombei DSM 6539T and T. petrolearius LAM0A37T, as performed by Illumina MiSeq, provides reference genomes for these respective species of Terrisporobacter for the first time. DNA-DNA hybridization values (d4) of MCA3T to Terrisporobacter glycolicus ATCC 14880T, T. petrolearius LAM0A37T and T. mayombei DSM 6539T are 48.8, 67.4 and 46.3 %, with cutoff value at 70 %. The type strain for T. hibernicus sp. nov. is MCA3T (=NCTC 14625T=LMG 32430T).

Clostridioides difficile as a Potential Pathogen of Importance to One Health: A Review.

Clostridioides difficile (basonym Clostridium) is a bacterial enteropathogen associated with cases of C. difficile infection that can result in pseudomembranous colitis, rapid fluid loss, and death. For decades following its isolation, C. difficile was thought to be a solely nosocomial pathogen, being isolated from individuals undergoing antimicrobial therapy and largely affecting elderly populations. More recently, C. difficile spores have been identified in the broader environment, including in food-producing animals, soil, and food matrices, in both ready-to-eat foods and meat products. Furthermore, evidence has emerged of hypervirulent ribotypes (RTs), such as RT078, similar to those cultured in asymptomatic carriers, also being identified in these environments. This finding may reflect on adaptations arising in these bacteria following selection pressures encountered in these niches, and which occurs due to an increase in antimicrobial usage in both clinical and veterinary settings. As C. difficile continues to adapt to new ecological niches, the taxonomy of this genus has also been evolving. To help understand the transmission and virulence potential of these bacteria of importance to veterinary public health, strategies applying multi-omics-based technologies may prove useful. These approaches may extend our current understanding of this recognized nosocomial pathogen, perhaps redefining it as a zoonotic bacterium. In this review, a brief background on the epidemiological presentation of C. difficile will be highlighted, followed by a review of C. difficile in food-producing animals and food products. The current state of C. difficile taxonomy will provide evidence of Clade 5 (ST11/RT078) delineation, as well as background on the genomic elements linked to C. difficile virulence and ongoing speciation. Recent studies applying second- and third-generation sequencing technologies will be highlighted, and which will further strengthen the argument made by many throughout the world regarding this pathogen and its consideration within a One Health dimension.

Management of Staple Line Leaks after Laparoscopic Sleeve Gastrectomy.

Background and Objectives: Laparoscopic sleeve gastrectomy has become one of the most popular bariatric surgeries in the United States with a low rate of morbidity and effective weight loss. However, staple line leak remains a feared complication requiring a lengthy and difficult treatment course until resolution. This study outlines the various treatment methods used within a high-volume bariatric practice for successful leak resolution without necessitating a conversion procedure. Methods: A retrospective review was conducted on all patients with staple line leak after laparoscopic sleeve gastrectomy in a three-surgeon bariatric practice from January 1, 2010 to December 31, 2019. Results: A total of 10 staple line leaks were identified with a leak rate of 0.9%. Patients presented on average 29.3 days postoperatively and were all diagnosed on computed tomography. Three patients were initially managed operatively with washout and drainage procedure. Six patients were managed endoscopically initially with either stent or over-the-scope clip placement. Most patients required multiple interventions with an average of 2.4 interventions per patient. Average time to leak resolution was 48.2 days (15-95 days). Conclusion: Management of staple line leaks after laparoscopic sleeve gastrectomy requires a multimodal approach usually requiring multiple interventions before leak resolution. We demonstrate effective utilization of varying interventions that lead to effective leak resolution and avoid conversion operations.

Antimicrobial resistance of Salmonella Indiana from retail chickens in China and emergence of an mcr-1-harboring isolate with concurrent resistance to ciprofloxacin, cefotaxime, and colistin.

Salmonella enterica serotype Indiana (S. Indiana) in Chinese poultry meat has aroused widespread concern because of its high prevalence and strong antimicrobial resistance. In consideration of the relationship in our previous study between S. Indiana and co-resistance to ciprofloxacin and cefotaxime (CIP-CTX), which were the first-line drug which were used in Salmonella infection in clinical, the antimicrobial resistance (AMR) of 224 CIP-CTX co-resistant S. Indiana isolated from retail chicken samples in China were investigated, with the aim of characterizing the AMR profiles and related resistance mechanisms to ciprofloxacin and cefotaxime among these CIP-CTX co-resistant S. Indiana isolates, all of which showed multi-drug-resistant (MDR) phenotypes. GyrA (S83F and D87N/G) with ParC (T57S and S80R) were the dominant amino acid substitution types, with oqxA, oqxB, and aac (6')-Ib-cr identified as common plasmid-mediated quinolone resistance (PMQR)-encoding genes. Five bla CTX-M gene subtypes were identified with bla CTX-M-65 ranking at the top. Equally important, we obtained one isolate CFSA664 harboring the mcr-1 gene was ESBL producer with co-resistance to nine in ten classes of tested drugs inclduing colistin. A single circular chromosome and 3 circular plasmids were found in its genome. Among the 26 AMR genes identified, 24 were located on plasmid pCFSA664-1, including three ESBL genes, while plasmid pCFSA664-3 owning only the mcr-1 gene and sharing the same backbone structure with plasmids from Enterobacteriaceae. No insertion sequences were found near the mcr-1 gene but a relaxase-encoding gene in the flank, which could transfer into E. coli J53 at a relatively high frequency. S. Indiana in this study exhibited highly drug-resistant phenotypes, contributing to the acceleration of the dissemination and emergence of this pathogen among different sources. Surveillance and a One Health strategy are needed to limit the emergence of S. Indiana along the food chain.

Is Laparoscopy Underutilized for Sigmoid Volvulus?

PURPOSE: Minimally invasive surgery has become increasingly prevalent. However, the majority of colectomies for volvulus are still performed via an open technique. The purpose of this study is to determine whether there is a difference in outcomes between laparoscopic and open procedures for sigmoid volvulus. MATERIALS AND METHODS: The American College of Surgeons National Surgical Quality Improvement Program and colectomy-targeted procedure databases were queried from 2013 to 2018. Patients undergoing partial colectomy without ileal resection for the indication of volvulus were compared based on approach (planned laparoscopic vs. planned open). The 2 groups were propensity score matched for perioperative variables. A subgroup analysis was performed comparing unplanned laparoscopic conversion to open (CTO) with planned open procedures. The primary outcomes were overall morbidity, mortality, and length of stay. RESULTS: Total 2493 patients were identified. Four hundred ninety-two cases began laparoscopically (20%), of which 391 were completed laparoscopically (79%). Laparoscopic approach was associated with longer operative times (133 vs. 104 min, P <0.001). Laparoscopic approach was associated with decreased overall morbidity (OR: 0.71, 95% CI, 0.54 to 0.93) and decreased length of stay when >7 days (OR: 0.70, 95% CI, 0.52 to 0.94). On subgroup analysis, there was no difference in outcomes when comparing unplanned CTO to planned open approach. CONCLUSIONS: Laparoscopic approach is used in a fraction of cases for colonic volvulus. When utilized, the majority are completed without CTO. Laparoscopy is associated with fewer complications and shorter hospital stays. Even with unplanned conversion to open, there is no difference in outcomes compared against planned open procedures. Surgeons should consider the utilization of laparoscopy for colonic volvulus.

Same day discharge does not lead to worse outcomes in patients undergoing uncomplicated laparoscopic foregut surgery.

INTRODUCTION: With the advancement of minimally invasive surgical techniques surgeons have moved away from elective open foregut surgeries. Despite studies demonstrating the safety of same day discharge in appropriate patient populations, ambulatory surgery has yet to be established as the practice norm for patients undergoing uncomplicated laparoscopic foregut surgery. METHODS: The ACS-NSQIP database was queried from 2005 to 2018 for patients who had undergone elective and non-emergent laparoscopic Heller myotomy, fundoplication, and paraesophageal hernia repairs with and without mesh. The primary endpoints in this study included number and severity of complications as classified by the Clavien-Dindo Classification, readmission, and return to the operating room. RESULTS: 6893 patients who met inclusion criteria were identified, 696 (10.1%) of which were discharged on the day of surgery. Patients who were discharged on post-operative day one were matched at a 3:1 ratio producing 2088 comparisons. There was no difference in overall morbidity (p = 0.264), readmission (OR 0.849, 95% CI 0.522-1.419), or return to the operating room (OR 1.15, 95% CI 0.531-2.761) between the two groups. CONCLUSION: Same day discharge for patients without life threatening comorbidities undergoing elective minimally invasive Heller myotomy, Nissen and Toupet fundoplication, and paraesophageal hernia repairs is safe and feasible.

Alterations in the Transcriptional Landscape Allow Differential Desiccation Tolerance in Clinical Cronobacter sakazakii.

Cronobacter sakazakii is a typical example of a xerotolerant bacterium. It is epidemiologically linked to low-moisture foods like powdered infant formula (PIF) and is associated with high fatality rates among neonates. We characterized the xerotolerance in a clinically isolated strain, Cronobacter sakazakii ATCC™29544T, and compared the desiccation tolerance with that of an environmental strain, C. sakazakii SP291, whose desiccation tolerance was previously characterized. We found that, although the clinical strain was desiccation-tolerant, the level of tolerance was compromised when compared with that of the environmental strain. Transcriptome sequencing (RNA-seq)-based deep transcriptomic characterization identified a unique transcriptional profile in the clinical strain compared with what was already known for the environmental strain. As RNA-seq was also carried out under different TSB growth conditions, genes that were expressed specifically under desiccated conditions were identified and denoted as desiccation responsive genes (DRGs). Interestingly, these DRGs included transcriptomic factors like fnr, ramA, and genes associated with inositol metabolism, a phenotype as yet unreported in C. sakazakii. Further, the clinical strain did not express the proP gene, which was previously reported to be very important for desiccation survival and persistence. Interestingly, analysis of the plasmid genes showed that the iron metabolism in desiccated C. sakazakii ATCC™29544T cells specifically involved the siderophore cronobactin, encoded by the iucABCD genes. Confirmatory studies using quantitative reverse transcription-PCR (qRT-PCR) determined that, though the secondary desiccation response genes were upregulated in C. sakazakii ATCC™29544T, the level of upregulation was lower than that in C. sakazakii SP291. All these factors may collectively contribute to the compromised desiccation tolerance in the clinical strain. IMPORTANCE Cronobacter sakazakii has led to outbreaks in the past, particularly associated with foods that are low in moisture content. This species has adapted to survive in low water conditions and can survive in such environments for long periods. These characteristics have enabled the pathogen to contaminate powder infant formula, a food matrix with which the pathogen has been epidemiologically associated. Even though clinically adapted strains can also be isolated, there is no information on how the clinical strains adapt to low moisture environments. Our research assessed the adaptation of a clinically isolated strain to low moisture survival on sterile stainless steel coupons and compared the survival with that of a highly desiccation-tolerant environmental strain. We found that, even though the clinical strain is desiccation-tolerant, the rate of tolerance was compromised compared with that of the environmental strain. A deeper investigation using RNA-seq identified that the clinical strain used pathways different from that of the environmental strain to adapt to low-moisture conditions. This shows that the adaptation to desiccation conditions, at least for C. sakazakii, is strain-specific and that different strains have used different evolutionary strategies for adaptation.

Characterisation of Early Positive mcr-1 Resistance Gene and Plasmidome in Escherichia coli Pathogenic Strains Associated with Variable Phylogroups under Colistin Selection.

An antibiotic susceptibility monitoring programme was conducted from 2004 to 2010, resulting in a collection of 143 Escherichia coli cultured from bovine faecal samples (diarrhoea) and milk-aliquots (mastitis). The isolates were subjected to whole-genome sequencing and were distributed in phylogroups A, B1, B2, C, D, E, and G with no correlation for particular genotypes with pathotypes. In fact, the population structure showed that the strains belonging to the different phylogroups matched broadly to ST complexes; however, the isolates are randomly associated with the diseases, highlighting the necessity to investigate the virulence factors more accurately in order to identify the mechanisms by which they cause disease. The antimicrobial resistance was assessed phenotypically, confirming the genomic prediction on three isolates that were resistant to colistin, although one isolate was positive for the presence of the gene mcr-1 but susceptible to colistin. To further characterise the genomic context, the four strains were sequenced by using a single-molecule long read approach. Genetic analyses indicated that these four isolates harboured complex and diverse plasmids encoding not only antibiotic resistant genes (including mcr-1 and bla) but also virulence genes (siderophore, ColV, T4SS). A detailed description of the plasmids of these four E. coli strains, which are linked to bovine mastitis and diarrhoea, is presented for the first time along with the characterisation of the predicted antibiotic resistance genes. The study highlighted the diversity of incompatibility types encoding complex antibiotic resistance elements such as Tn6330, ISEcp1, Tn6029, and IS5075. The mcr-1 resistance determinant was identified in IncHI2 plasmids pCFS3273-1 and pCFS3292-1, thus providing some of the earliest examples of mcr-1 reported in Europe, and these sequences may be a representative of the early mcr-1 plasmidome characterisation in the EU/EEA.

Antimicrobial Resistance and Genomic Characterization of Two mcr-1-Harboring Foodborne Salmonella Isolates Recovered in China, 2016.

The mcr-1 gene mediating mobile colistin resistance in Escherichia coli was first reported in China in 2016 followed by reports among different species worldwide, especially in E. coli and Klebsiella. However, data on its transmission in Salmonella are still lacking. This study analyzed the antimicrobial resistance (AMR) profiles and the mcr-1 gene presence in 755 foodborne Salmonella from 26 provinces of mainland, China in 2016. Genomic features of two mcr-1-carrying isolates, genome sequencing, serotypes and further resistance profiles were studied. Among the 755 Salmonella tested, 72.6% were found to be resistant to at least one antimicrobial agent and 10% were defined as multi-drug resistant (MDR). Salmonella Derby CFSA231 and Salmonella Typhimurium CFSA629 were mcr-1-harboring isolates. Both expressed an MDR phenotype and included a single circular chromosome and one plasmid. Among the 22 AMR genes identified in S. Derby CFSA231, only the mcr-1 gene was localized on the IncX4 type plasmid pCFSA231 while 20 chromosomal AMR genes, including four plasmid-mediated quinolone resistance (PMQR) genes, were mapped within a 64 kb Salmonella genomic island (SGI) like region. S. Typhimurium CFSA629 possessed 11 resistance genes including an mcr-1.19 variant and two ESBL genes. Two IS26-flanked composite-like transposons were identified. Additionally, 153 and 152 virulence factors were separately identified in these two isolates with secretion system and fimbrial adherence determinants as the dominant virulence classes. Our study extends our concern on mcr-1-carrying Salmonella in regards to antimicrobial resistance and virulence factors, and highlight the importance of surveillance to mitigate dissemination of mcr-encoding genes among foodborne Salmonella.

Analysis of the Oxidative Stress Regulon Identifies soxS as a Genetic Target for Resistance Reversal in Multidrug-Resistant Klebsiella pneumoniae.

In bacteria, the defense system deployed to counter oxidative stress is orchestrated by three transcriptional factors, SoxS, SoxR, and OxyR. Although the regulon that these factors control is known in many bacteria, similar data are not available for Klebsiella pneumoniae. To address this data gap, oxidative stress was artificially induced in K. pneumoniae MGH78578 using paraquat and the corresponding oxidative stress regulon recorded using transcriptome sequencing (RNA-seq). The soxS gene was significantly induced during oxidative stress, and a knockout mutant was constructed to explore its functionality. The wild type and mutant were grown in the presence of paraquat and subjected to RNA-seq to elucidate the soxS regulon in K. pneumoniae MGH78578. Genes that are commonly regulated both in the oxidative stress and soxS regulons were identified and denoted as the oxidative SoxS regulon; these included a group of genes specifically regulated by SoxS. Efflux pump-encoding genes and global regulators were identified as part of this regulon. Consequently, the isogenic soxS mutant was found to exhibit a reduction in the minimum bactericidal concentration against tetracycline compared to that of the wild type. Impaired efflux activity, allowing tetracycline to be accumulated in the cytoplasm to bactericidal levels, was further evaluated using a tetraphenylphosphonium (TPP+) accumulation assay. The soxS mutant was also susceptible to tetracycline in vivo in a zebrafish embryo model. We conclude that the soxS gene could be considered a genetic target against which an inhibitor could be developed and used in combinatorial therapy to combat infections associated with multidrug-resistant K. pneumoniae. IMPORTANCE Antimicrobial resistance is a global health challenge. Few new antibiotics have been developed for use over the years, and preserving the efficacy of existing compounds is an important step to protect public health. This paper describes a study that examines the effects of exogenously induced oxidative stress on K. pneumoniae and uncovers a target that could be useful to harness as a strategy to mitigate resistance.

Emergence of a Salmonella enterica serovar Typhimurium ST34 isolate, CFSA629, carrying a novel mcr-1.19 variant cultured from egg in China.

OBJECTIVES: This study aimed to characterize the genomic features of a Salmonella enterica serovar Typhimurium ST34 isolate, CFSA629, which carried a novel mcr-1 variant, designated as mcr-1.19, mapped to an ESBL-encoding IncHI2 plasmid. METHODS: Antimicrobial susceptibility assays as well as WGS were carried out on isolate CFSA629. The complete closed genome was obtained and then explored to obtain genomic features. Plasmid sequence comparison was performed for pCFSA629 with similar plasmids and the mcr-1 genetic environment was analysed. RESULTS: S. Typhimurium ST34 CFSA629 expressed an MDR phenotype to six classes of compound and consisted of a single circular chromosome and one plasmid. It possessed 11 resistance genes including 2 ESBL genes that mapped to the chromosome and the plasmid; an IS26-flanked composite-like transposon was identified. A novel mcr-1 variant (mcr-1.19) was identified, which had a unique SNP (G1534A) that gave rise to a novel MCR-1 protein containing a Val512Ile amino acid substitution. Plasmid pCFSA629 possessed a conjugative plasmid transfer gene cluster as well as an antimicrobial resistance-encoding gene cluster-containing region that contained two IS26 composite-like transposonal modules, but was devoid of any plasmid-mediated quinolone resistance genes. The background of mcr-1.19 consisted of an ISApl1-mcr-1-PAP2-ter module. CONCLUSIONS: We report on an MDR S. Typhimurium ST34 CFSA629 isolate cultured from egg in China, harbouring an mcr-1.19 variant mapped to an IncHI2 plasmid. This highlights the importance of surveillance to mitigate dissemination of mcr-encoding genes among foodborne Salmonella. Improved surveillance is important for tackling the dissemination of mcr genes among foodborne Salmonella around the world.

Yersinia occitanica is a later heterotypic synonym of Yersinia kristensenii subsp. rochesterensis and elevation of Yersinia kristensenii subsp. rochesterensis to species status.

The taxonomic position of Yersinia kristensenii subsp. rochesterensis and Yersinia occitanica was re-evaluated by genomic analysis. Average nucleotide identity (ANI), digital DNA-DNA hybridization values, and phylogenetic analyses of the type strains indicate that Y. kristensenii subsp. rochesterensis and Y. occitanica are the same genospecies. Additionally, the overall genomic relatedness index (OGRI) values reveal that Y. kristensenii subsp. rochesterensis should be elevated to species status as Yersinia rochesterensis sp. nov.

Role of Negative Pressure Wound Therapy When Performing Elective Open Colectomy.

Background: The impact of negative pressure wound therapy (NPWT) as an adjunct to colorectal surgery is largely unknown. The purpose of this study was to determine whether NPWT impacts wound complications during elective open colectomy. Methods: The American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) and colectomy targeted procedure databases were queried from 2012-2018 for patients undergoing non-emergent planned open colectomies. Groups were propensity score matched for anastomosis type (ileo-colic, colo-colic, colo-rectal), age, body mass index (BMI), diabetes, smoking, steroid use, wound classification, American Society of Anesthesiologists (ASA) class, operative time, and wound layers closed. Wound complications were defined as superficial surgical site infection (SSI), deep incisional SSI, and dehiscence. Results: A total of 15,770 patients were identified; 92 underwent simultaneous NPWT (0.58%). Non-NPWT patients were matched at a 5:1 ratio, producing 460 comparisons. There was no difference in wound complications (8.26% non-NPWT vs. 6.52% NPWT; p = 0.574). In addition, there were no differences in wound complications when only including patients who had NPWT placed over closed skin (9.11% non-NPWT vs. 7.25% NPWT; p = 0.789). On multivariable analysis, NPWT was not associated with wound complications (odds ratio [OR] 0.79; 95% confidence interval [CI], 0.37-1.69). Conclusions: Negative pressure wound therapy does not reduce wound complications in open elective colectomies. Large randomized studies and more granular data are needed to ascertain if there is any benefit in select patient populations.

Time to weigh in on obesity and associated comorbidities in combat-wounded amputees.

BACKGROUND: The Joint Trauma System database estimates that about 1,200 individuals have sustained a combat-related amputation during the Global War on Terror. Previous retrospective studies have demonstrated that combat-related amputees develop obesity and cardiovascular disease, but the incidence of obesity and associated comorbidities in this population is unknown. The objectives of this study are to determine the prevalence of obesity in the military amputee population and to compare this with the general population. METHODS: This is a retrospective review of 978 patients who sustained a combat-related amputation from 2003 to 2014. Prevalence of obesity and comorbid conditions were determined. A multivariate logistic regression model was performed to identify risk factors for postamputation obesity. Kaplan-Meier curves were constructed using obesity as the event of interest. RESULTS: A total of 1,233 charts were reviewed with 978 patients included for analysis. The median age of injury was 24 years. Median follow-up time was 8.7 years, ranging from 0.5 years to 16.9 years. The average Injury Severity Score was 23.3. The average body mass index preinjury was 25.6 kg/m2, and the average most recent corrected body mass index was found to be 31.4 kg/m2. Prevalence of comorbidities was higher in the amputee population. Fifty percent of patients who progressed to obesity did so within 1.3 years. CONCLUSION: There is a notable prevalence of obesity that develops in the amputee population that is much higher than the general population. We determined that the amputee population is at risk, and these patients should be closely monitored for 1 to 2.5 years following injury. This study provides a targeted period for which monitoring and intervention can be implemented. LEVEL OF EVIDENCE: Retrospective, basic science, outcomes analysis, level III/IV.

3D printing of face shields to meet the immediate need for PPE in an anesthesiology department during the COVID-19 pandemic.

BACKGROUND: Anesthesia providers are at risk for contracting COVID-19 due to close patient contact, especially during shortages of personal protective equipment. We present an easy to follow and detailed protocol for producing 3D printed face shields and an effective decontamination protocol, allowing their reuse. METHODS: The University of Nebraska Medical Center (UNMC) produced face shields using a combination of 3D printing and assembly with commonly available products, and produced a simple decontamination protocol to allow their reuse. To evaluate the effectiveness of the decontamination protocol, we inoculated bacterial suspensions of E. coli and S. aureus on to the face shield components, performed the decontamination procedure, and finally swabbed and enumerated organisms onto plates that were incubated for 12-24 hours. Decontamination effectiveness was evaluated using the average log10 reduction in colony counts. RESULTS: Approximately 112 face shields were constructed and made available for use in 72 hours. These methods were successfully implemented for in-house production at UNMC and at Tripler Army Medical Center (Honolulu, Hawaii). Overall, the decontamination protocol was highly effective against both E. coli and S. aureus, achieving a ≥4 log10 (99.99%) reduction in colony counts for every replicate from each component of the face shield unit. DISCUSSION: Face shields not only act as a barrier against the soiling of N95 face masks, they also serve as more effective eye protection from respiratory droplets over standard eye shields. Implementation of decontamination protocols successfully allowed face shield and N95 mask reuse, offering a higher level of protection for anesthesiology providers at the onset of the COVID-19 pandemic. CONCLUSIONS: In a time of urgent need, our protocol enabled the rapid production of face shields by individuals with little to no 3D printing experience, and provided a simple and effective decontamination protocol allowing reuse of the face shields.

Comparative genomic insights into Yersinia hibernica - a commonly misidentified Yersinia enterocolitica-like organism.

Food-associated outbreaks linked to enteropathogenic Yersinia enterocolitica are of concern to public health. Pigs and their meat are recognized risk factors for transmission of Y. enterocolitica. This study aimed to describe the comparative genomics of Y. enterocolitica along with a number of misclassified Yersinia isolates, now constituting the recently described Yersinia hibernica. The latter was originally cultured from an environmental sample taken at a pig slaughterhouse. Unique features were identified in the genome of Y. hibernica, including a novel integrative conjugative element (ICE), denoted as ICEYh-1 contained within a 255 kbp region of plasticity. In addition, a zebrafish embryo infection model was adapted and applied to assess the virulence potential among Yersinia isolates including Y. hibernica.

Epidemiological and genetic characterization of Clostridium butyricum cultured from neonatal cases of necrotizing enterocolitis in China.

OBJECTIVE: Laboratory-based characterization and traceback of Clostridium butyricum isolates linked to outbreak cases of neonatal necrotizing enterocolitis (NEC) in a hospital in China. METHODS: In total, 37 samples were collected during the NEC outbreak. Classical bacteriological methods were applied to isolate and identify Clostridium spp. Meanwhile, 24 samples collected after an outbreak were similarly tested. All Clostridium isolates were identified to species level as either C. butyricum or C. sporogenes. These isolates were subsequently subtyped using pulsed-field gel electrophoresis (PFGE). Genomic DNA was purified from 2 representative C. butyricum isolates and sequenced to completion. RESULTS: Of 37 samples collected during the NEC outbreak, 17 (45.95%) were positive for Clostridium spp. One species, C. butyricum, was cultured from 10 samples. Another species cultured from 2 other samples was identified as C. sporogenes. Both of these species were cocultured from 5 samples. Pulsotyping showed that the 15 C. butyricum and the 7 C. sporogenes isolates produced indistinguishable DNA profiles. No NEC cases were reported after disinfection following the outbreak, and all samples collected after the outbreak were negative for Clostridium spp. Whole-genome sequencing (WGS) indicated that sialidase, hemolysin, and enterotoxin virulence factors were located on the chromosomes of 2 C. butyricum isolates. CONCLUSIONS: The outbreak of NEC was epidemiologically linked to C. butyricum contamination within the hospital. This is the first report of an NEC outbreak associated with C. butyricum infection in China.

Yersinia canariae sp. nov., isolated from a human yersiniosis case.

A Gram-negative rod from the Yersinia genus was isolated from a clinical case of yersiniosis in the United Kingdom. Long read sequencing data from an Oxford Nanopore Technologies (ONT) MinION in conjunction with Illumina HiSeq reads were used to generate a finished quality genome of this strain. Overall Genome Related Index (OGRI) of the strain was used to determine that it was a novel species within Yersinia, despite biochemical similarities to Yersinia enterocolitica. The 16S ribosomal RNA gene accessions are MN434982-MN434987 and the accession number for the complete and closed chromosome is CP043727. The type strain is SRR7544370T (=NCTC 14382T/=LMG 31573T).