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).

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.

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.

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.

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.

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.

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.

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).

Biological Impact of a Large-Scale Genomic Inversion That Grossly Disrupts the Relative Positions of the Origin and Terminus Loci of the Streptococcus pyogenes Chromosome.

A large-scale genomic inversion encompassing 0.79 Mb of the 1.816-Mb-long Streptococcus pyogenes serotype M49 strain NZ131 chromosome spontaneously occurs in a minor subpopulation of cells, and in this report genetic selection was used to obtain a stable lineage with this chromosomal rearrangement. This inversion, which drastically displaces the ori site relative to the terminus, changes the relative length of the replication arms so that one replichore is approximately 0.41 Mb while the other is about 1.40 Mb in length. Genomic reversion to the original chromosome constellation is not observed in PCR-monitored analyses after 180 generations of growth in rich medium. Compared to the parental strain, the inversion surprisingly demonstrates a nearly identical growth pattern in the first phase of the exponential phase, but differences do occur when resources in the medium become limited. When cultured separately in rich medium during prolonged stationary phase or in an experimental acute infection animal model (Galleria mellonella), the parental strain and the invertant have equivalent survival rates. However, when they are coincubated together, both in vitro and in vivo, the survival of the invertant declines relative to the level for the parental strain. The accompanying aspect of the study suggests that inversions taking place near oriC always happen to secure the linkage of oriC to DNA sequences responsible for chromosome partition. The biological relevance of large-scale inversions is also discussed.IMPORTANCE Based on our previous work, we created to our knowledge the largest asymmetric inversion, covering 43.5% of the S. pyogenes genome. In spite of a drastic replacement of origin of replication and the unbalanced size of replichores (1.4 Mb versus 0.41 Mb), the invertant, when not challenged with its progenitor, showed impressive vitality for growth in vitro and in pathogenesis assays. The mutant supports the existing idea that slightly deleterious mutations can provide the setting for secondary adaptive changes. Furthermore, comparative analysis of the mutant with previously published data strongly indicates that even large genomic rearrangements survive provided that the integrity of the oriC and the chromosome partition cluster is preserved.

Susceptibility (re)-testing of a large collection of Listeria monocytogenes from foods in China from 2012 to 2015 and WGS characterization of resistant isolates.

OBJECTIVES: Our aim was to determine the antimicrobial susceptibilities of 2862 Listeria monocytogenes cultured from various foods in China and to use WGS to characterize the antimicrobial resistance and virulence genotypes of those expressing a resistance phenotype. METHODS: The susceptibilities of 2862 L. monocytogenes were determined by broth microdilution. Twenty-eight L. monocytogenes were found to be resistant to one to four antibiotics. All 28 resistant isolates were subsequently sequenced using short-read high accuracy protocols. The corresponding genomes were assembled and further analysis was carried out using appropriate bioinformatics pipelines. RESULTS: All 28 resistant L. monocytogenes were classified into five STs (ST3, ST8, ST9, ST155 and ST515). Both ST9 and ST155 were dominant and their genotypes correlated with their resistance phenotypes. All ST9 isolates were MDR and could be phylogenetically classified into two clusters. One was relatively close to clinical origins and one to food. Downstream analysis of the genetic contexts in which these resistance genotypes were found suggested that these may have been acquired from other bacteria by horizontal transfer or insertion into the chromosome. All isolates harboured Listeria pathogenicity island (LIPI)-1 and LIPI-2, and only two harboured LIPI-3. CONCLUSIONS: This study reported on the antimicrobial susceptibilities of 2862 foodborne L. monocytogenes along with the genomic characterization of 28 resistant isolates, 11 of which expressed an MDR phenotype. These data showed that this bacterium can acquire resistance by horizontal gene transfer in and between species. This study may necessitate a re-evaluation of risk to public health, associated with this bacterial species.

RNA Sequencing-Based Transcriptional Overview of Xerotolerance in Cronobacter sakazakii SP291.

Cronobacter sakazakii is a xerotolerant neonatal pathogen epidemiologically linked to powdered infant food formula, often resulting in high mortality rates. Here, we used transcriptome sequencing (RNA-seq) to provide transcriptional insights into the survival of C. sakazakii in desiccated conditions. Our RNA-seq data show that about 22% of the total C. sakazakii genes were significantly upregulated and 9% were downregulated during desiccation survival. When reverse transcription-quantitative PCR (qRT-PCR) was used to validate the RNA-seq data, we found that the primary desiccation response was gradually downregulated during the tested 4 hours of desiccation, while the secondary response remained constitutively upregulated. The 4-hour desiccation tolerance of C. sakazakii was dependent on the immediate microenvironment surrounding the bacterial cell. The removal of Trypticase soy broth (TSB) salts and the introduction of sterile infant formula residues in the microenvironment enhanced the desiccation survival of C. sakazakii SP291. The trehalose biosynthetic pathway encoded by otsA and otsB, a prominent secondary bacterial desiccation response, was highly upregulated in desiccated C. sakazakiiC. sakazakii SP291 ΔotsAB was significantly inhibited compared with the isogenic wild type in an 8-hour desiccation survival assay, confirming the physiological importance of trehalose in desiccation survival. Overall, we provide a comprehensive RNA-seq-based transcriptional overview along with confirmation of the phenotypic importance of trehalose metabolism in Cronobacter sakazakii during desiccation.IMPORTANCECronobacter sakazakii is a pathogen of importance to neonatal health and is known to persist in dry food matrices, such as powdered infant formula (PIF) and its associated production environment. When infections are reported in neonates, mortality rates can be high. The success of this bacterium in surviving these low-moisture environments suggests that Cronobacter species can respond to a variety of environmental signals. Therefore, understanding those signals that aid the persistence of this pathogen in these ecological niches is an important step toward the development of strategies to reduce the risk of contamination of PIF. This research led to the identification of candidate genes that play a role in the persistence of this pathogen in desiccated conditions and, thereby, serve as a model target to design future strategies to mitigate PIF-associated survival of C. sakazakii.

Yersinia hibernica sp. nov., isolated from pig-production environments.

A Gram-stain-negative, rod-shaped strain isolated from pig-production environments was identified as a new species within the genus Yersinia using multifaceted genomic and biochemical approaches. The genome of this strain was closed using a hybrid assembly approach combining both high accuracy short read sequencing data with long read sequencing technology. Phylogenetic analysis of the 16S rRNA gene showed ~98 % similarity to Yersinia kristensenii and ~98 % similarity to Yersinia enterocolitica. Average nucleotide identity (OrthoANI) values were calculated as 85.79 % to Y. kristensenii ATCC 33638T and 85.73 % to Y. enterocolitica ATCC 9610T thereby providing evidence that this isolate should be considered as a novel species. The type strain is CFS1934T (=NCTC 14222T=LMG 31076T).

Outcomes of robot-assisted versus laparoscopic repair of small-sized ventral hernias.

INTRODUCTION: The aim of the study is to investigate the outcomes of the da Vinci robot-assisted laparoscopic hernia repair of small-sized ventral hernias with circumferential suturing of the mesh compared to the traditional laparoscopic repair with trans-fascial suturing. METHODS: A retrospective review was conducted of all robot-assisted umbilical, epigastric and incisional hernia repairs performed at our institution between 2013 and 2015 compared to laparoscopic umbilical or epigastric hernia repairs. Patient characteristics, operative details and postoperative complications were collected and analyzed using univariate analysis. Three primary minimally invasive fellowship trained surgeons performed all of the procedures included in the analysis. RESULTS: 72 patients were identified during the study period. 39 patients underwent robot- assisted repair (21 umbilical, 14 epigastric, 4 incisional), and 33 patients laparoscopic repair (27 umbilical, 6 epigastric). Seven had recurrent hernias (robot: 4, laparoscopic: 3). There were no significant differences in preoperative characteristics between the two groups. Average operative time was 156 min for robot-assisted repair and 65 min for laparoscopic repair (p < 0.0001). The average defect size was significantly larger for the robot group [3.07 cm (1-9 cm)] than that for the laparoscopic group [2.02 cm (0.5-5 cm)] (p < 0.0001), although there was no significant difference in the average size of mesh used (13 vs. 13 cm). There was no difference in patients requiring postoperative admission or length of stay between the two groups. The mean duration of follow-up was 47 days. There was no difference in complication rate during this time, and no recurrences were reported. CONCLUSION: There are no significant differences in terms of safety and early efficacy when comparing small-sized ventral hernias repaired using the robot-assisted technique versus the standard laparoscopic repair.

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.

Retrograde intussusception seven years after a laparoscopic Roux-en-Y gastric bypass.

Intussusception after Roux-en-Y gastric bypass is more common than previously believed. It usually occurs between one and three years post-operatively, though we present a case that presented with a retrograde intussusception necessitating bowel resection seven years after a laparoscpic Roux-en-Y gastric bypass. The diagnosis and etiological theories are discussed based on findings from the literature.

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.

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.

Whole-genome association study on tissue tropism phenotypes in group A Streptococcus.

Group A Streptococcus (GAS) has a rich evolutionary history of horizontal transfer among its core genes. Yet, despite extensive genetic mixing, GAS strains have discrete ecological phenotypes. To further our understanding of the molecular basis for ecological phenotypes, comparative genomic hybridization of a set of 97 diverse strains to a GAS pangenome microarray was undertaken, and the association of accessory genes with emm genotypes that define tissue tropisms for infection was determined. Of the 22 nonprophage accessory gene regions (AGRs) identified, only 3 account for all statistically significant linkage disequilibrium among strains having the genotypic biomarkers for throat versus skin infection specialists. Networked evolution and population structure analyses of loci representing each of the AGRs reveal that most strains with the skin specialist and generalist biomarkers form discrete clusters, whereas strains with the throat specialist biomarker are highly diverse. To identify coinherited and coselected accessory genes, the strength of genetic associations was determined for all possible pairwise combinations of accessory genes among the 97 GAS strains. Accessory genes showing very strong associations provide the basis for an evolutionary model, which reveals that a major transition between many throat and skin specialist haplotypes correlates with the gain or loss of genes encoding fibronectin-binding proteins. This study employs a novel synthesis of tools to help delineate the major genetic changes associated with key adaptive shifts in an extensively recombined bacterial species.