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Abstract Klebsiella pneumoniae multidrug-resistant (MDR) high-risk clones drive the spread of antimicrobial resistance (AMR) associated infections, resulting in limited therapeutic options. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa. Representative carbapenem-resistant [K. pneumoniae carbapenemase (KPC)-2, New-Delhi metallo-beta (β)-lactamase (NDM)-1, oxacillinase (OXA)-181, OXA-232, OXA-48, Verona integron-encoded metallo-β-lactamase (VIM)-1] K. pneumoniae isolates (n = 22) obtained from inpatient and outpatient’s urine (n = 9) and inpatients rectal carriage (n = 13) were selected for short-read whole genome sequencing. Klebsiella pneumoniae population include sequence type (ST)-307 (n = 3), ST2497 (n = 5) and ST17 (n = 4). The ST17 strains were exclusively obtained from rectal screening. Ten isolates co-harboured carbapenemase genes including β-lactamase gene encoding KPC-2 + OXA-181, NDM-1 + OXA-48 and NDM-1 + OXA-181. One ST307 isolate (UP-KT-73CKP) co-harboured three carbapenemase genes (bla NDM-1 + bla OXA-48 + bla OXA-181), while all the ST2497 strains co-harboured (bla NDM-1 + bla OXA-232). Phenotypically, hypermucoviscosity was observed in a single ST307 isolate. The ST307 isolate UP-KT-151UKP harboured colibactin genotoxins. The following mobile genetic elements were detected: plasmids [incompatibility group (Inc)-FIB(K), IncX3], and bacteriophages [e.g. Klebsi_ST16_OXA48phi5.4_NC_049450, Klebsi_3LV2017_NC_047817(36)]. The study highlights the importance of local genomic surveillance systems to characterise K. pneumoniae MDR high-risk clones. This data will aid in designing infection and prevention measures for limiting the spread of carbapenemase-producing K. pneumoniae in Gauteng, South Africa.

Purpose This study was performed to assess the risk factors for artificial urinary sphincter (AUS) explantation in a large multicenter cohort. Methods We retrospectively reviewed the medical records for all 1,233 implantations of the AMS-800 AUS device in male nonneurological patients from 2005 to 2020 across 13 French centers. Patients with neurological conditions were excluded from the study. To identify factors associated with explantation-free survival, survival analysis was performed. Explantation was defined as the complete removal of the device, whereas revision referred to the replacement of the device or its components. Results The study included 1,107 patients, of whom 281 underwent AUS explantation. The median survival without explantation was 83 months. The leading causes of explantation were infection and erosion. Univariate analysis revealed several significant risk factors for explantation: age above 75 years (34.6% in the explanted group vs. 25.8% in the nonexplanted group, P=0.007), history of radiotherapy (43.5% vs. 31.3%, P=0.001), and anticoagulant use (15% vs. 8.6%, P

ABSTRACT IncF plasmids are commonly found in extra-intestinal pathogenic Escherichia coli (ExPEC) strains, serving as reservoirs for antimicrobial resistance (AMR) genes and virulence factors, persistently coexisting with ExPEC lineages. Multidrug-resistant (MDR) high-risk ExPEC clones, particularly ST131, ST1193, and ST410, have acquired diverse IncF plasmids over time, containing various AMR determinants, contributing significantly to their global success. However, the broader roles of these IncF plasmids in the success of MDR ExPEC clones, beyond AMR, remain elusive. In this study, we employed a novel clustered regularly interspaced short palindromic repeats–CRISPR-associated protein-9 nuclease (CRISPR-Cas9)-mediated pCasCure plasmid-curing system to precisely remove specific IncF plasmids among ExPEC clones (ST1193, ST131, and ST410). Antibiotic-resistant parent strains reverted to antibiotic-susceptible states post-curing; however, IncF plasmid curing did not show significant impact on bacterial in vitro growth and had little impact on other in vitro phenotypes, including survival in water, dry environment and biofilm production. In addition, IncF plasmid curing did not affect the conjugation frequency of KPC-producing pKpQIL plasmid. This study represents a pivotal initial step in understanding the precise roles of IncF plasmids in the success of ExPEC. Future research will be crucial in investigating their influence on cell invasion and in vivo fitness, thereby providing a more comprehensive perspective on the functions of IncF plasmids in MDR ExPEC clones. IMPORTANCE Understanding the role of IncF plasmids in the success of drug-resistant bacteria has far-reaching implications for tackling antibiotic resistance. The study's use of a novel CRISPR-Cas9-mediated plasmid-curing system provides a precision tool for dissecting the specific impact of IncF plasmids on ExPEC clones, especially high-risk, multidrug-resistant strains like ST131, ST1193, and ST410. The study offers a crucial stepping stone for future research into understanding how these plasmids influence more complex aspects of bacterial behavior, such as cell invasion and in vivo fitness.

Abstract Epidemic IncF plasmids have been pivotal in the selective advantage of multidrug-resistant (MDR) extraintestinal pathogenic Escherichia coli (ExPEC). These plasmids have offered several advantages to their hosts that allowed them to coevolve with the bacterial host genomes and played an integral role in the success of ExPEC. IncF plasmids are large, mosaic, and often contain various types of antimicrobial resistance (AMR) and virulence associated factor (VAF) genes. The presence of AMR, VAF genes, several addition/restriction systems combined with truncated transfer regions, led to the fixation of IncF plasmids in certain ExPEC MDR clones, such as ST131 and ST410. IncF plasmids entered the ST131 ancestral lineage in the mid 1900s and different ST131 clade/CTX-M plasmid combinations coevolved over time. The IncF_CTX-M-15/ST131-C2 subclade combination emerged during the early 2000s, spread rapidly across the globe, and is one of the greatest clone/plasmid successes of the millennium. The ST410-B3 subclade containing bla CTX-M-15 incorporated the NDM-5 carbapenemase gene into existing IncF platforms, providing an additional positive selective advantage that included the carbapenems. A “plasmid-replacement” clade scenario occurred in the histories of ST131 and ST410 as different subclades gained different AMR genes on different IncF platforms. The use of antimicrobial agents will generate selection pressures that enhance the risks for the continuous emergence of MDR ExPEC clone/IncF plasmid combinations. The reasons for clade/IncF replacements and associations between certain clades and specific IncF plasmid types are unknown. Such information will aid in designing management and prevention strategies to combat AMR.

Carbapenems are effective options available for treating serious infections caused by multi-drugresistant (MDR) Enterobacterales bacteria (1). The emergence of carbapenem resistance is a major public health concern, and the World [...]

We describe the global molecular epidemiology of 229 carbapenemase-producing Escherichia coli in 36 countries during 2015–2017. Common carbapenemases were oxacillinase (OXA) 181 (23%), New Delhi metallo-β-lactamase (NDM) 5 (20%), OXA-48 (17%), Klebsiella pneumoniae carbapenemase 2 (15%), and NDM-1 (10%). We identified 5 dominant sequence types (STs); 4 were global (ST410, ST131, ST167, and ST405), and 1 (ST1284) was limited to Turkey. OXA-181 was frequent in Jordan (because of the ST410-B4/H24RxC subclade) and Turkey (because of ST1284). We found nearly identical IncX3-blaOXA-181 plasmids among 11 STs from 12 countries. NDM-5 was frequent in Egypt, Thailand (linked with ST410-B4/H24RxC and ST167-B subclades), and Vietnam (because of ST448). OXA-48 was common in Turkey (linked with ST11260). Global K. pneumoniae carbapenemases were linked with ST131 C1/H30 subclade and NDM-1 with various STs. The global carbapenemase E. coli population is dominated by diverse STs with different characteristics and varied geographic distributions, requiring ongoing genomic surveillance.

This study investigated the molecular characteristics of urinary carbapenemase-producing Klebsiella pneumoniae isolates (n = 194) in Gauteng, South Africa, using simple, cost-effective PCR methodologies. Extensively drug resistant (XDR) ST307 with blaOXA-181 on IncX3 plasmids was endemic in Gauteng community hospitals leaving limited options for treating in- and outpatient urinary tract infections. High-level ceftazidime/avibactam resistance was detected among isolates harbouring blaOXA-48-like including blaOXA-181. These findings highlighted the need for genomic methodologies suitable for lower- and middle-income countries to track XDR clones and plasmids in community hospitals. Such results will aid with treatment and stewardship strategies. [ABSTRACT FROM AUTHOR]

IntroductionExtended spectrum beta-lactamase (ESBL) producing Escherichia coli have become widespread among food producing animals. These strains serve as a reservoir of antibiotic resistance genes (ARGs) and act as a possible source of infection to humans as transmission can occur by direct or indirect contact.MethodsThis study investigated the faecal carriage of ESBL producing and colistin resistant E. coli in poultry over a 2-year period (2017-2019) from Zimbabwe. A total of 21 ESBL positive isolates from poultry cloacal specimens were selected for whole genome sequencing from animal E. coli isolates bio-banked at the National Microbiology Reference laboratory using phenotypic susceptibility testing results from the National Escherichia coli Surveillance Program to provide representation of different geographical regions and year of isolation. Cloacal swabs were collected from 3000 broiler live birds from farm 1 and from farm 2, 40 backyard chickens and 10 ducks were sampled. Antimicrobial susceptibility and ESBL testing were performed as per Clinical Laboratory Standards Institute guidelines. Whole genome sequencing of ESBL producing isolates was used to determine sequence types (STs), ARGs, and phylogroups.ResultsTwenty-one of the included E. coli isolates were confirmed as ESBL producers. Three defined sequence type clonal complexes (CCs) were identified (ST10CC, ST155CC and ST23CC), with ST10CC associated with the most antibiotic resistant profile. The ESBL phenotype was linked to the presence of either cefotaximase-Munich-14 (CTX-M-14) or CTX-M-79. Plasmid mediated quinolone resistant determinants identified were qnrB19 and qnrS1 and one ST10CC isolate from farm 1 broiler chickens harbored a mobile colistin resistance gene (mcr-1). Phylogenetic groups most identified were B1, A and unknown.DiscussionsThe avian ESBL producing E. coli belonged to a diverse group of strains. The detection of several ARGs highlights the importance of implementing enhanced control measures to limit the spread in animals, environment, and humans. This is the first report of mcr-1 in Zimbabwe, which further underscores the importance of the One Health approach to control the spread and development of AMR.

Oligonucleotides and nucleic acid analogues that alter gene expression are now showing therapeutic promise in human disease. Whilst the modification of synthetic nucleic acids to protect against nuclease degradation and to influence drug function is common practice, such modifications may also confer unexpected physicochemical and biological properties. Gapmer mixed-modified and DNA oligonucleotides on a phosphorothioate backbone can bind non-specifically to intracellular proteins to form a variety of toxic inclusions, driven by the phosphorothioate linkages, but also influenced by the oligonucleotide sequence. Recently, the non-antisense or other off-target effects of 2′ O- fully modified phosphorothioate linkage oligonucleotides are becoming better understood. Here, we report chemistry-specific effects of oligonucleotides composed of modified or unmodified bases, with phosphorothioate linkages, on subnuclear organelles and show altered distribution of nuclear proteins, the appearance of highly stable and strikingly structured nuclear inclusions, and disturbed RNA processing in primary human fibroblasts and other cultured cells. Phosphodiester, phosphorodiamidate morpholino oligomers, and annealed complimentary phosphorothioate oligomer duplexes elicited no such consequences. Disruption of subnuclear structures and proteins elicit severe phenotypic disturbances, revealed by transcriptomic analysis of transfected fibroblasts exhibiting such disruption. Our data add to the growing body of evidence of off-target effects of some phosphorothioate nucleic acid drugs in primary cells and suggest alternative approaches to mitigate these effects.

Global expansion of antimicrobial drug–resistant Escherichia coli sequence type (ST) 131 is unrivaled among human bacteria. Understanding trends among ST131 clades will help with designing prevention strategies. We screened E. coli from blood samples (n = 1,784) obtained in Calgary, Alberta, Canada, during 2006, 2012, and 2016 by PCR for ST131 and positive samples (n = 344) underwent whole-genome sequencing. The incidence rate per 100,000 residents increased from 4.91 during 2006 to 12.35 during 2012 and 10.12 during 2016. ST131 belonged to clades A (10%), B (9%), and C (81%). Clades C1-nonM27 and B were common during 2006, and C2 containing blaCTX-M-15, C1-M27 containing blaCTX-M-27, and A were responsible for the increase of ST131 during 2012 and 2016. C2 was the most antimicrobial drug–resistant subclade and increased exponentially over time. Eradicating ST131, more specifically the C2 subclade, will lead to considerable public health benefits for persons in Calgary.

NISSEN fundoplication is a common procedure for the management of gastroesophageal reflux disease. It can have the side effect of a ''gas bloat syndrome'', an accumulation of air responsible for functional symptoms and gastric distension. Gastric necrosis due to gastric distension is a rare event, but with a high mortality rate in case of delayed diagnosis.We describe the surgical management of a partial necrosis of the stomach in a 13-year-old boy with mental retardation. Exploratory laparotomy revealed extensive gastric necrosis without perforation. We performed a partial gastrectomy, without removal of the NISSEN, with reinstatement of gastrostomy, drainage and antibiotic therapy. A posterosuperior gastric fistula appeared in following, leading us to perform a feeding jejunostomy.After three months, the patient was able to return home, fed on the jejunostomy.This is the first pediatric case of partial necrosis of the stomach in the aftermath of a NISSEN, managed by partial gastrectomy. In case of suspected gastric necrosis, an emergency laparotomy associated with a digestive resection procedure seems to be the most indicated. Our case proves that even in case of extensive necrosis, a partial gastrectomy more or less associated with a controlled fistulation can be attempted.

Escherichia coli sequence type (ST) 131 is the quintessential example of a successful, global, antimicrobial-resistant, high-risk clone among human bacteria (1,2). Currently, ST131 is the most common global extraintestinal pathogenic [...]

ABSTRACT Escherichia coli is a leading cause of community-acquired and health care-associated bloodstream infections (BSIs) worldwide. Limited information is available regarding the changes in population dynamics of human E. coli over extended time periods, especially among nonbiased E. coli isolates in large well-defined geographical regions. Coque and colleagues (I. Rodríguez, A. S. Figueiredo, M. Sousa, S. Aracil-Gisbert, et al., mSphere 6:e00868-21, 2021, https://doi.org/10.1128/msphere.00868-21) conducted a longitudinal study of E. coli BSIs in a Madrid hospital over a 21-year period (1996 to 2016). Certain E. coli B2 phylogroups (i.e., ST131 and ST73) dominated the community E. coli population in Madrid. These community clones were often introduced into the hospital setting. This study and other longitudinal surveys from England and Canada showed that ST131 subclades C1 and C2 were mainly responsible for the increase in fluoroquinolone and cephalosporin resistance among E. coli during the mid- to late 2000s.

Purpose: This study was performed to assess the risk factors for artificial urinary sphincter (AUS) explantation in a large multicenter cohort. Methods: We retrospectively reviewed the medical records for all 1,233 implantations of the AMS-800 AUS device in male nonneurological patients from 2005 to 2020 across 13 French centers. Patients with neurological conditions were excluded from the study. To identify factors associated with explantation-free survival, survival analysis was performed. Explantation was defined as the complete removal of the device, whereas revision referred to the replacement of the device or its components. Results: The study included 1,107 patients, of whom 281 underwent AUS explantation. The median survival without explantation was 83 months. The leading causes of explantation were infection and erosion. Univariate analysis revealed several significant risk factors for explantation: age above 75 years (34.6% in the explanted group vs. 25.8% in the nonexplanted group, P=0.007), history of radiotherapy (43.5% vs. 31.3%, P=0.001), and anticoagulant use (15% vs. 8.6%, P<0.001). In logistic regression analysis, the only significant risk factor was previous radiotherapy (odds ratio [OR], 2.05; P<0.05). Cox proportional hazards analysis revealed 2 factors associated with earlier explantation: transcorporal cuff implantation (hazard ratio [HR], 2.67; P=0.01) and the annual caseload of the center (HR, 1.08; P=0.02). When specifically examining explantation due to erosion, radiotherapy was the sole factor significantly associated with the risk of erosion (OR, 2.47; P<0.05) as well as earlier erosion (HR, 1.90; P=0.039). Conclusions: In this series, conducted in a real-world setting across multiple centers with different volumes and levels of expertise, the median survival without AUS explantation was 83 months. This study confirms that radiotherapy represents the primary independent risk factor for AUS erosion in male nonneurological patients. [ABSTRACT FROM AUTHOR]

Purpose: The emergence of carbapenem-resistant P. aeruginosa (CRPA) harbouring acquired carbapenemase genes (blaVIM, blaIMP and blaNDM) has become a global public health threat. Three CRPA isolates included in the study had an extensively drug-resistant phenotype with susceptibility to colistin only and were positive for the blaNDM-1 gene. The current study aimed to investigate the genomic epidemiology and molecular characteristics of the blaNDM-1-positive CRPA isolates collected from the Gauteng region, South Africa. Methods: Short read whole genome sequencing (WGS) was performed to determine sequence types (STs), genetic relatedness, resistome, virulome and the genetic environment of the blaNDM-1 gene. Results: The WGS and phylogenetic analyses revealed that the study isolates belonged to an international high-risk clone ST773 and belonged to the same clade with eight blaNDM-1-positive ST773 isolates from Hungary, India, Nigeria, South Korea and USA. The study isolates harboured a wide repertoire of intrinsic and acquired antibiotic resistance genes (ARGs) related with mobile genetic elements, porins and efflux pumps, as well as virulence factor genes. The clade-specific ARGs (blaNDM-1, floR2/cmlA9, rmtB4, tetG) were found in a putative integrative and conjugative element (ICE) region similar to ICE6660-like. Conclusion: As ICE carrying the blaNDM-1 gene can easily spread to other P. aeruginosa isolates and other Gram-negative bacteria, the findings in this study highlight the need for appropriate management strategies and active surveillance of CRPA isolates in the Gauteng region, South Africa. [ABSTRACT FROM AUTHOR]

Klebsiella pneumoniae sequence type (ST) 307 is an emerging global antimicrobial drug–resistant clone. We used whole-genome sequencing and PCR to characterize K. pneumoniae ST307 with oxacillinase (OXA) 181 carbapenemase across several private hospitals in South Africa during 2014–2016. The South Africa ST307 belonged to a different clade (clade VI) with unique genomic characteristics when compared with global ST307 (clades I–V). Bayesian evolution analysis showed that clade VI emerged around March 2013 in Gauteng Province, South Africa, and then evolved during 2014 into 2 distinct lineages. K. pneumoniae ST307 clade VI with OXA-181 disseminated over a 15-month period within 42 hospitals in 23 cities across 6 northeastern provinces, affecting 350 patients. The rapid expansion of ST307 was most likely due to intrahospital, interhospital, intercity, and interprovince movements of patients. This study highlights the importance of molecular surveillance for tracking emerging antimicrobial clones.

Abstract Background Blood stream infections (BSIs) cause a complex cascade of inflammatory events, resulting in significant morbidity and mortality in children in Tanzania. This study was designed to delineate circulating bacterial species, antimicrobial resistance (AMR) profiles and risk factors for BSIs and mortality among children in the cascade of referral health care facilities so as to guide comprehensive BSIs management. Methods A multiple cross sectional analytical study was conducted between July 20, 2016 to October 04, 2017 involving 950 children less than five years of age in the North-western part of Tanzania. Children with clinical features suggestive of BSIs were included. Demographic, clinical and laboratory information on culture and antimicrobial susceptibility testing was collected from children; and analyzed using STATA version 13.0 software. Results The prevalence of BSIs among children was 14.2% (95% CI: 12.1–16.6%), with specific prevalence in the district, regional and tertiary hospitals being 8.3, 6.4 and 20.0%, respectively. The most common bacterial pathogens isolated from 135 culture-positive children were Klebsiella pneumoniae (55, 40.4%), Staphylococcus aureus (23, 17.0%), and Escherichia coli (17, 12.6%). Multi-drug resistance (MDR) was higher in isolates from children at Bugando Medical Centre (BMC) tertiary hospital than isolates from district and regional hospitals [OR (95% CI): 6.36 (2.15–18.76); p = 0.001]. Independent risk factors for BSIs were neonatal period [OR (95% CI): 1.93 (1.07–3.48); p = 0.003] and admission at BMC [2.01 (1.08–3.74); p = 0.028)]. Approximately 6.6% (61/932) of children died, and risk factors for mortality were found to be children attending BMC [OR (95% CI): 4.95 (1.95–12.5); p = 0.001)], neonatal period [OR (95% CI): 2.25 (1.02–5.00); p = 0.045)], and children who had blood culture positive results [OR (95% CI): 1.95 (1.07–3.56); p = 0.028)]. Conclusions The prevalence of BSIs (14.2%) in this multi-centre study is high and predominantly caused by the MDR K. pneumoniae. Priority interventional measures to combat BSIs and mortality, specifically among neonates at BMC are urgently recommended.