BackgroundThe Enterobacter cloacae complex (ECC) is increasingly recognized as a major opportunistic pathogen in healthcare-associated infections (HAIs), particularly in intensive care settings. Its clinical relevance has risen in parallel with the global spread of MDR strains, including carbapenemase producers, which complicate management and contribute to excess morbidity, prolonged hospitalization and increased healthcare costs. Outbreaks caused by ECC are often traced to contaminated water systems, medical devices, or the hands of healthcare workers, but reports from low and middle income countries (LMICs) remain scarce. In August–September 2023, a cluster of ECC infections was detected at a Level-1 trauma centre in northern India. An urgent epidemiological and microbiological investigation was undertaken to delineate transmission dynamics, identify reservoirs and guide infection prevention and control (IPC) measures.MethodsWe conducted a prospective outbreak investigation of all culture-confirmed ECC cases occurring ≥48 h after admission during August–September 2023. Cases were identified in real time and reported in parallel with implementation of control measures. Clinical and epidemiological data included demographics, comorbidities, prior antibiotic exposure, invasive device use and outcomes. Environmental surveillance targeted high-risk areas such as water sources, sinks, taps and hand swabs from healthcare workers. Antimicrobial susceptibility testing (AST) was performed using standard protocols. Infection prevention and control (IPC) interventions included reinforcement of hand hygiene, environmental decontamination, chlorination and treatment of hospital water systems, and central line-associated bloodstream infection (CLABSI) care bundles. WGS was undertaken on 10 representative isolates (5 clinical, 5 environmental) to determine clonal relatedness, sequence types, plasmid profiles and antimicrobial resistanceResultsA total of 19 developed ECC infections; 63% were admitted to the ICU. No deaths occurred. Prior antibiotic exposure was reported in 68% and invasive procedures in 74%. Median ICU stay among infected patients was 14 days compared to 8 days in non-ICU cases (P=0.03). Environmental surveillance yielded 52 ECC isolates: 60% from healthcare worker hand swabs and 40% from hospital water samples. All isolates were resistant to cefuroxime. 80% were susceptible to amikacin, meropenem, imipenem, cefepime, tigecycline and cotrimoxazole. WGS showed clonal dissemination of ST97 (60%) and ST171 (40%) with >99.8% identity between clinical and environmental isolates. Plasmids IncX3_1 and IncFII(pECLA)_1_pECLA carried blaNDM, blaACT-5 and blaSHV. Genes oqxA/oqxB (100%) and fosA (68%) were detected. Following IPC interventions, ECC incidence decreased from 15.8 to 6.7 cases per 1000 patient-days (P<0.05). Water contamination fell from 40% to 10%, and hand hygiene compliance improved from 60% to 85%. No additional cases occurred after September 2023.ConclusionsThis outbreak was driven by clonal dissemination of ECC, primarily through water systems and healthcare worker hands. WGS provided high resolution evidence linking clinical and environmental isolates, enabling targeted interventions. The multimodal IPC response including reinforced hand hygiene, water decontamination and central line care bundles successfully reduced transmission and contained the outbreak. However, residual water contamination highlights the resilience of ECC in biofilm-associated reservoirs. Our findings underscore the value of integrating genomic epidemiology into outbreak investigations in LMIC settings and the need for sustained environmental monitoring.

The alert for emergence of pig-associated MRSA ST 398 in multi-regions China.

BackgroundAcinetobacter baumannii is one of the most common causes of healthcare-acquired infections, particularly among the critically ill patients in intensive care units (ICUs). Its multidrug‐resistance (MDR) nature is a major factor contributing to treatment difficulties, and ultimately increased patient mortality. This study aimed to investigate the prevalence, antimicrobial resistance patterns, and molecular characteristics of A. baumannii strains isolated from ICU patients (non-COVID-19) in Tehran, Iran.ResultsThe infection rate of A. baumannii among ICU patients was 2.25% (75/3340). More than 90% of isolates showed resistance to key antibiotics including imipenem, meropenem, cefotaxime, and ciprofloxacin. Colistin was the most effective drug, with a susceptibility rate of 61.3%. The majority of the isolates (92%) were categorized as extensively drug-resistant (XDR) and harbored multiple antibiotic resistance genes (ARGs). Among carbapenem resistance genes, blaOXA-23-like was the most prevalent, detected in 72% (54/75) of isolates, followed by blaOXA-24-like in 49.3% (37/75). Regarding aminoglycoside resistance, the genes aac(6')-Ib and ant(2')-Ia were identified in 66.6% (50/75) and 32% (24/75) of the isolates, respectively. Genotyping by multiplex PCR revealed that most of isolates (85.3%) belonged to GC2. Furthermore, REP-PCR genotyping identified eight different genotypes, with one dominant genotype accounting for 81% (51/63) of isolates.ConclusionThe present study demonstrates the predominance of XDR A. baumannii strains carrying diverse ARGs in our ICU setting. These findings raise concern, as such strains complicate treatment, limit therapeutic options, and may contribute to poor outcomes in critically ill patients. Mortality was high and appeared more associated with extensive resistance than with comorbidities. The clonal dissemination of these strains further emphasizes the need for robust infection control measures. Implementation of strict infection control measures and robust antibiotic stewardship programs remains essential to limit the spread of these highly resistant pathogens.

Clonal dissemination of ST19 Salmonella Typhimurium within a Chinese poultry breeding pyramid and One-Health implications.

Genome-wide insight into the evolution and global transmission of tigecycline resistant tet(X4)-carrying Klebsiella species across reservoirs.

Drug-resistant Acinetobacter baumannii poses a global health crisis, especially in Asia. It has a propensity to become clonally endemic in healthcare settings. However, its clonal distribution in a broad geographic area is unclear. The clonality of A. baumannii was characterized nationwide by collecting 572 drug-resistant A. baumannii from 18 hospitals across Thailand regions between 2017-2018 and genotyping them by random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) in association with carbapenemase genes data. The results depicted 12 types of RAPD banding. Strikingly, two types were predominant in all hospitals (79%). Of those, 96% harbored the blaOXA-23 gene. The banding pattern matched the preexisting strain in the institution, suggesting an ongoing nationwide circulation of the resistant clone. Interestingly, a unique banding type was identified in high proportion in two nearby hospitals in the northern region (21%, 53/252). Two isolates with the same banding pattern were also identified in a hospital in Bangkok, suggesting the possibility of transfer between regions. Most of the subset of isolates analyzed belonged to sequence type (ST) 2, the most prominent ST in the Asia-Pacific region. This study demonstrated continuous dissemination of predominating A. baumannii clones across the country, and the emergence of endemic hospital-specific clones, all with high burdens of blaOXA-23; suggesting a strong selection for these resistance determinants. In addition, genotyping with RAPD can be a simple and cost-effective epidemiological tool with efficient discriminatory power for A. baumannii in developing countries.

ObjectivesTo investigate the antimicrobial resistance mechanisms and intra-hospital clonal dissemination of carbapenem-resistant ST477 Klebsiella michiganensis.MethodsBetween 14 December 2019 and 23 August 2020, six K. michiganensis isolates producing NDM-type carbapenemases were recovered from Jilin Provincial People’s Hospital in China. Antimicrobial susceptibility was determined using the broth microdilution method. Whole-genome sequencing (WGS) was performed for all isolates. Sequence typing (ST), resistance genes, and plasmid types were identified using the PubMLST, ResFinder, and PlasmidFinder databases, respectively. Conjugation experiments were conducted to assess plasmid transferability. Additionally, 344 publicly available K. michiganensis genomes were retrieved and used to construct a phylogenetic tree based on core-genome single nucleotide polymorphisms (SNPs).ResultsWGS revealed that all six isolates belonged to ST477 and harbored blaNDM-1, blaSFO-1, and blaVEB-3. The maximum pairwise difference among the six isolates was only 8 SNPs, indicating clonal transmission. Antimicrobial susceptibility testing showed high-level resistance to imipenem, meropenem, and ceftazidime-avibactam, while susceptibility was retained to amikacin, aztreonam-avibactam, eravacycline, tigecycline, and colistin. Conjugation assays confirmed that the blaNDM-1-carrying plasmid was self-transmissible. Clinical data showed that four of the six patients had a history of transfer to the intensive care unit (ICU). Phylogenetic analysis combined with resistance gene profiling based on publicly available genomes revealed that 50% (175/350) of K. michiganensis isolates from human hosts carried carbapenem resistance genes. Notably, Isolates from China exhibited a higher carriage rate of carbapenemase genes (76.1%, 51/67). No ST477-related genomes were identified in current public datasets.ConclusionsThis study is the first to report the clonal dissemination of ST477 K. michiganensis harboring blaNDM-1 in a Chinese hospital.

BackgroundCarbapenem‐resistant Klebsiella pneumoniae (CRKP) poses a critical threat to public health due to its ability to accumulate multidrug‐resistance (MDR) and to spread silently via gastrointestinal carriage. While hospital‐associated CRKP has been well documented, little is known about its prevalence and clonal dynamics among outpatients.MethodsIn this cross‐sectional study, 300 stool samples were collected from outpatients without any gastrointestinal symptoms from April to September 2023. K. pneumoniae isolates were recovered on imipenem‐supplemented MacConkey agar and identified by biochemical testing. Antimicrobial susceptibility was determined by disk diffusion and broth microdilution tests. ESBLs and predominant carbapenemase genes were detected by PCR. Clonal relatedness was evaluated by PCR‐based ompK36 typing and multi-locus sequence typing (MLST).ResultsForty K. pneumoniae isolates (13.3% carriage rate) were obtained, of which 45% considered as CRKP, while over 50% exhibited MDR profiles. ESBLs and carbapenemase genes were prevalent as follows: blaSHV (87.5%), blaTEM (55%), blaCTX-M-15 (37.5%), blaNDM-1 (22.5%), blaOXA-48 (27.5%), and blaKPC-2 (0%). An elevated imipenem minimum inhibitory concentration (MIC) > 128 µg/mL was observed. The ompK36 group D variants, which are associated with this high level of resistance, predominated (30%). MLST identified ST231 as the sole lineage among OXA-48 and NDM-1 producers.ConclusionFecal carriage of CRKP among outpatients is both common and driven by highly resistant, high‐risk clones—most notably ST231—underscoring the emergence of community reservoirs. Integrated One Health surveillance, expanded antimicrobial stewardship beyond hospitals, and targeted infection control measures are urgently needed to curb dissemination of CRKP.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12879-025-11670-3.

Antimicrobial susceptibility of Clostridioides difficile. An Argentinian multicenter study of isolates from human patients.

Prevalence and molecular epidemiology of optrA-positive Enterococcus in herders and yaks from high-altitude Tibet, China.

Healthcare-associated infections (HAIs), particularly in neonatal intensive care units (NICUs), pose significant challenges due to neonates' vulnerability and the rapid infection spread. However, risk factors facilitating pathogen persistence and dissemination have not been comprehensively investigated. This study aims to track HAI transmission pathways in NICUs and identify key risk factors contributing to the persistence and spread of carbapenem-resistant Klebsiella pneumoniae (CRKP). We analyzed CRKP epidemiology and population dynamics in neonatal patients at a pediatric hospital in China over 8 years. Random forest models identified primary risk factors for CRKP persistence and outbreaks, focusing on clonal spread, healthcare groups (HGs), and plasmid dynamics. Three major clonal outbreaks involving ST14 and ST433 strains were identified, highlighting the critical role of clonal dissemination in NICUs. Complex transmission patterns, characterized by periods of dormancy and resurgence, suggest the existence of underlying reservoirs. HGs were implicated in the short-term transmission of CRKP, with >80% of infection clusters involving patients from the same HG. Plasmids emerged as critical factors in the long-term persistence of CRKP, with shifts in plasmid prevalence corresponding to outbreak periods. This study advances our understanding of CRKP transmission dynamics in NICUs, highlighting the multifaceted roles of clonal dissemination, HGs, and plasmid-mediated persistence. Our findings emphasize the need for enhanced infection control measures targeting both intra- and inter-group transmissions and plasmid surveillance. IMPORTANCE This study provides a detailed analysis of carbapenem-resistant Klebsiella pneumoniae (CRKP) transmission dynamics in neonatal intensive care units (NICUs) over eight years, utilizing 64 isolates and applying machine learning to identify risk factors associated with persistence and spread. Through phylogenetic analyses, we uncovered three clonal outbreaks and linked healthcare group (HG) interactions, bacterial genotypes, and plasmid prevalence to short- and long-term CRKP transmission. We identified that HGs are primary mediators of rapid, short-term transmission, while specific plasmids play an extended role in maintaining CRKP presence across multiple patient cohorts and bacterial strains. This finding suggests the existence of latent reservoirs or periodic reintroductions from external sources, thus reshaping the understanding of NICU-associated pathogen transmission and persistence.

Antimicrobial resistance (AMR) mediated by extended-spectrum β-lactamases (ESBLs) is a growing global concern, particularly among Enterobacteriaceae. The CTX-M-type ESBLs, encoded by the blaCTX-M gene, are of significant public health importance due to their high prevalence and broad geographic distribution. Typically located on plasmids and often co-occurring with other AMR genes, blaCTX-M contributes to multidrug resistance (MDR). However, increasing evidence suggests secondary chromosomal integration of blaCTX-M, sometimes alongside other resistance determinants. The extent and implications of this mechanism remain poorly characterized, especially in Africa, where genomic surveillance is limited. In this study, we retrieved 295 chromosomal sequences of Enterobacteriaceae of African origin from the GenBank and performed in silico predictions of blaCTX-M and other AMR genes. blaCTX-M-carrying sequences were further characterized by in silico multilocus sequence typing and genome annotation. Chromosomal insertions were identified through alignment with reference genomes. Overall, 47 of 295 sequences (15.9%) harbored the blaCTX-M gene, with the highest prevalence in Klebsiella pneumoniae (29/157, 18.5%), followed by Escherichia coli (13/72, 18.1%), Enterobacter spp. (4/38, 10.5%), and Shigella spp. (1/12, 8.3%). The most common allele was blaCTX-M-15 (31/47, 66.0%), followed by blaCTX-M-14 (12/47, 25.5%), blaCTX-M-55 (3/47, 6.4%), and blaCTX-M-27 (1/27, 3.7%). Co-occurrence of blaCTX-M with additional AMR genes was frequently observed, with integration events often associated with mobile genetic elements such as ISEcp1 and IS26. Notably, strains from the same hospital setting were phylogenetically related and shared sequence types and AMR gene profiles, suggesting local clonal dissemination. These findings reveal a notable presence of chromosomally integrated blaCTX-M among African Enterobacteriaceae, frequently in association with other resistance genes, thereby facilitating stable MDR propagation independent of plasmid maintenance. This evolutionary adaptation may have significant implications for the persistence and spread of MDR in clinical settings.

blaNDM-5-encoding ST171 Enterobacter hormaechei: A global genomic and epidemiological perspective.

Metagenomic and whole-genome characterization of carbapenem-resistant Acinetobacter baumannii carrying blaOXA-23 gene within the Tn2006 transposon among ICU patients.

Evolution and epidemiology of pks+Klebsiella pneumoniae: Global and local insights.

Unveiling the clonal dynamics and transmission mechanism of carbapenem-resistant Klebsiella pneumoniae in the ICU environment.

Antimicrobial resistance in Pseudomonas aeruginosa is of increasing concern in Canada, leading to limited treatment options and poor clinical outcomes. Herein we characterized carbapenem-resistant P. aeruginosa identified through the Canadian national surveillance program CANWARD. Antimicrobial susceptibility for 1725 P. aeruginosa isolates was assessed using broth microdilution and 2024 CLSI breakpoints. WGS of carbapenem-resistant isolates was used to identify STs, resistance and virulence markers. Genetic relatedness was further assessed using cgMLST for select STs. From 2018 to 2023, CANWARD collected 1725 P. aeruginosa isolates, of which 371 (21.5%) were carbapenem-resistant. The majority of carbapenem-resistant P. aeruginosa were isolated from respiratory specimens of male patients aged 18-65 years living in central Canada. Only 0.8% (n = 3) of the carbapenem-resistant isolates harboured a carbapenemase gene. WGS identified mutations associated with OprD dysfunction, MexAB-OprM efflux and AmpC overexpression in 73.6%, 1.1% and 4.9% of isolates, respectively. Most isolates (98.1%) harboured at least one of the following class D β-lactamase genes: OXA-2, OXA-5, OXA-10 or OXA-50-like subfamily. Wide genetic diversity was observed with 151 different STs identified. The most common STs were ST17 (4.6%), ST27 (4.6%) and high-risk clones ST235 (4.3%), ST244 (3.5%), ST253 (6.4%) and ST357 (2.7%). cgMLST clusters were identified amongst 34.9% of the high-risk clones, suggesting clonal dissemination. Currently, >20% of clinical isolates of P. aeruginosa in Canada are carbapenem-resistant. Genetic evidence indicates that clonal dissemination of high-risk clones is occurring in Canada. High-risk clones are virulent and often MDR. Continued surveillance of P. aeruginosa is important.

Background: The emergence and spread of the tigecycline resistance gene tet(A)-v1 in carbapenem-resistant Klebsiella pneumoniae (CRKP) poses significant public health challenges. However, the prevalence of tet(A)-v1-positive CRKP, especially in pediatric patients, remains poorly understood. This study aims to address the gap by performing an in-depth analysis of isolates collected from a children’s hospital in China. Methods: A 4-year retrospective study was conducted in the children’s hospital in Suzhou, China. Non-duplicated specimens were obtained from pediatric patients, and antimicrobial susceptibility profiles were assessed. Whole-genome sequencing and bioinformatics analyses were conducted to characterize the genetic background, antimicrobial resistance determinants, hypervirulence-associated genes, diversity of tet(A)-v1-carrying plasmids, the genetic environment of tet(A)-v1, and the potential for clonal transmission. Conjugative transferability of tet(A)-v1-carrying plasmids was also evaluated via conjugation assays. Results: Of the 73 tet(A)-v1-positive CRKP isolates from pediatric patients, 10.96% were non-susceptible to tigecycline. These isolates exhibited high genetic diversity, spanning across 13 STs (sequence types), with ST17 being predominant. Three carbapenemases were identified, with IMP being the most common. Isolates from diverse backgrounds, such as ST17, ST20, ST323, ST792, and ST3157, demonstrated evidence of clonal transmission. The tet(A)-v1 gene was located on 14 distinct plasmids across seven replicon types, with IncFIA/IncHI1 and IncFII being most commonly detected. All tet(A)-v1-carrying plasmids were multidrug-resistant, and 68.49% were conjugatively transferable, indicating a high potential for horizontal transfer. Four genetic contexts bordering tet(A)-v1 were identified, which points to active clonal dissemination. Conclusions: Although limited to a single hospital, this study represents one of the first in-depth investigations of tet(A)-v1-positive CRKP in pediatric patients, providing valuable insights into the prevalence and spread of tet(A)-v1 in this vulnerable group. These findings emphasize the urgent need for enhanced surveillance and infection control measures to curb the spread of tet(A)-v1-positive CRKP in pediatric healthcare environments, offering critical insights to mitigate its public health impact.

The global emergence of multidrug- and pandrug-resistant Klebsiella pneumoniae poses a critical threat to public health, particularly in hospital settings. This study describes a nosocomial outbreak caused by K. pneumoniae in a tertiary-care hospital in Mexico and provides a comprehensive genomic analysis of six clinical isolates. All isolates exhibited pandrug resistance, including carbapenems and colistin. Whole-genome sequencing identified 37 antimicrobial resistance genes, including blaNDM-1, blaOXA-1, blaCTX-M-15, and a pmrB R256G mutation associated with colistin resistance. Two conjugative plasmids (pAA046 and pAA276) carried multiple resistance genes and mobile genetic elements. Although all isolates harbored CRISPR-Cas type I-E systems, no spacers matched resistance plasmids, suggesting functional inactivity. Capsular typing identified the KL27 locus with the wzi187 allele. Phylogenetic and cgMLST analyses confirmed clonal dissemination and close genetic relatedness to strains from Europe and the USA. Despite the absence of classical hypervirulence markers, the presence of kfu, fimH, and mrkD genes indicates adaptation to the hospital environment. These findings confirm the clonal spread of pandrug-resistant K. pneumoniae ST392-KL27 in a Mexican hospital, underscoring the role of plasmid-mediated resistance and the potential for global dissemination.

Genomic analysis of a multisite metastatic prostate cancer cohort reveals patterns of clonal heterogeneity, dissemination, and evolution, highlighting the need to evaluate multiple samples to fully characterize the clonal architecture of tumors. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI .