Prevalent Clone Research Articles

The clinical characteristics and molecular epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) among very elderly people in Japan.

Methicillin-resistant Staphylococcus aureus (MRSA) is a major nosocomial infection-causing pathogen. The clonal shift from staphylococcal cassette chromosome mec (SCCmec) type II MRSA to SCCmec type IV MRSA has occurred rapidly in acute-care hospitals. However, the epidemiology and clinical impacts of MRSA in geriatric hospitals are poorly documented. We performed a molecular epidemiological analysis of the clinical isolates and retrospectively investigated the clinical characteristics of SCCmec type IV MRSA in elderly individuals. MRSA isolates were grouped according to the SCCmec type and virulence genes (tst, sea, seb, sec, and lukS/F-PV), and multi-locus sequence typing (MLST) was performed. Of the 145 MRSA isolates obtained from patients with a median age of 85 years, 100 (69.0%) were obtained from sputum samples, 22 (15.2%) from skin and soft tissues, and seven (4.8%) from blood samples. The most prevalent clone was SCCmec type IV/clonal complex (CC)1/sea+ (59.3%), followed by SCCmec type I/sequence type (ST) 8 (17.3%). Of the 17 (11.7%) strains to which an anti-MRSA drug was administered by a physician, only three were SCCmec type IV/CC1/sea+ (17.6%) and five were SCCmec type I/ST8 (29.4%). SCCmec type IV/CC1/sea+ MRSA was more frequently isolated in long-term care wards than were SCCmec type I/ST8 strains (odds ratio: 2.85, 95% confidence interval: 1.08-7.54) and was less frequently treated as the cause of MRSA infections (odds ratio: 0.15, 95% confidence interval: 0.03-0.73). SCCmec type IV/CC1/sea+ MRSA was the predominant clone and could be easily transmissible and be capable of colonization. Geriatr Gerontol Int 2023; 23: 744-749.

Epidemiological characteristics of multidrug-resistant Acinetobacter baumannii ST369 in Anhui, China.

Acinetobacter baumannii is of growing concern for global health owing to its ability to evade the immune system and develop resistance to antibiotics. We analyzed A. baumannii using the National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/pathogens) database and observed that the ST369 strain isolated in China constituted over 50% of the globally prevalent ST369 clones. This finding highlights the significant impact of ST369 on public health in China. In this study, we examined eight strains of multidrug-resistant A. baumannii ST369 isolated from a provincial hospital in China. We conducted whole-genome sequencing, comparative genomic analysis, and phenotypic experiments, and used the Galleria mellonella infection model to achieve a comprehensive understanding of the organism. In our study, we identified two mutations, G540A and G667D, on the wzc gene of A. baumannii ST369 that can potentially affect bacterial virulence and viscosity. We also verified the impact of these mutations on virulence and resistance. In addition, we examined two proteins, AB46_0125 and AB152_03903, which may play a role in virulence. These findings establish a foundation for future studies on clinical ST369 isolates harboring such mutations. IMPORTANCE Acinetobacter baumannii is a major health threat due to its antibiotic resistance and ability to cause nosocomial infections. Epidemiological studies indicated that the majority of globally prevalent ST369 clones originated from China, indicating a significant impact on public health in the country. In this study, we conducted whole-genome sequencing, comparative genomics, and Galleria mellonella infection model on eight A. baumannii ST369 isolates collected from a provincial hospital in China to comprehensively understand the organism. We identified two mutations (G540A and G667D) on the wzc gene that can affect bacterial virulence and viscosity. We confirmed their impact on resistance and virulence. We also investigated the potential involvement of AB46_0125 and AB152_03903 proteins in virulence. This finding provides a theoretical reference for further research on A. baumannii ST369 clinical isolates with similar mutations.

Antibiotic susceptibility and clonal distribution of Staphylococcus aureus from pediatric skin and soft tissue infections: 10-year trends in multicenter investigation in China.

Skin and Soft Tissue Infections (SSTIs) Surveillance Network of S. aureus In Pediatrics in China was established in 2009 to routinely report epidemiological changes. We aimed to monitor the present antibiotic sensitivity and molecular characteristics of S. aureus and methicillin-resistant S. aureus (MRSA) from SSTIs in children nationwide and track the changes over the past decade. Patients diagnosed with SSTIs from the dermatology departments of 22 tertiary pediatric hospitals in seven geographical regions of China were recruited continuously from May 2019 to August 2021. S. aureus was isolated, and its sensitivity to 15 antimicrobials was evaluated using the broth microdilution method. The molecular characteristics of the MRSA isolates were determined through multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing. The presence of the Panton-Valentine leukocidin gene (pvl) was determined. The detection rate of S. aureus was 62.57% (1379/2204), among which MRSA accounted for 14.79% (204/1379), significantly higher than the result in previous study in 2009-2011 (2.58%, 44/1075). Compared with previous study, the sensitivity to cephalosporins and fusidic acid decreased to varying degrees, while that to chloramphenicol, ciprofloxacin, clindamycin, erythromycin, gentamicin, penicillin, and tetracycline increased significantly. The sensitivity to mupirocin, trimethoprim/sulfamethoxazole (TRISUL), and rifampicin still maintained at a high level (97.90%, 99.35% and 96.66% respectively). The leading multidrug resistance pattern of MRSA and methicillin-sensitive S. aureus (MSSA) were erythromycin-clindamycin-tetracycline (55.84%; 43/77) and erythromycin-clindamycin-chloramphenicol (27.85%, 44/158) respectively. 12 high-level mupirocin-resistant strains were detected, and notable differences in geographical distribution and seasonal variation were observed. The main types of MRSA were ST121 (46.08%, 94/204), followed by ST59 (19.61%, 40/204). SCCmec V (65.69%, 134/204) and SCCmec IV (31.86%, 65/204) were dominant epidemic types. ST121-V, ST59-IV, and ST22-V were the most prevalent clones nationwide. The detection rate of pvl had increased markedly from 9.09% (4/44) in 2009-2011 to 22.55% (46/204) in 2019-2021 (P<0.05). The antibiotic sensitivity and molecular characteristics of S. aureus from pediatric SSTIs has changed significantly over the past decade. To standardize medical care, provide timely and reasonable clinical treatment, and effectively manage infection control, Chinese pediatric SSTIs guidelines are urgently needed.

Transmission of livestock-associated methicillin-resistant Staphylococcus aureus between animals, environment, and humans in the farm.

Staphylococcus aureus (S. aureus) is a fearsome bacterial pathogen that can colonize and infect humans and animals. Depending on the different sources, MRSA is classified as hospital-associated methicillin-resistant S. aureus (HA-MRSA), community-associated MRSA (CA-MRSA), and livestock-associated MRSA (LA-MRSA). LA-MRSA is initially associated with livestock, and clonal complexes (CCs) were almost always 398. However, the continued development of animal husbandry, globalization, and the widespread use of antibiotics have increased the spread of LA-MRSA among humans, livestock, and the environment, and other clonal complexes such as CC9, CC5, and CC8 have gradually emerged in various countries. This may be due to frequent host switching between humans and animals, as well as between animals. Host-switching is typically followed by subsequent adaptation through acquisition and/or loss of mobile genetic elements (MGEs) such as phages, pathogenicity islands, and plasmids as well as further host-specific mutations allowing it to expand into new host populations. This review aimed to provide an overview of the transmission characteristics of S. aureus in humans, animals, and farm environments, and also to describe the main prevalent clones of LA-MRSA and the changes in MGEs during host switching.

Global distribution and genomic characteristics of tet(X)-positive Escherichia coli among humans, animals, and the environment

In recent years, the plasmid-mediated transmission of the tigecycline resistance gene tet(X) in Escherichia coli has received considerable attention. However, studies on the global distribution of tet(X)-positive E. coli remain scarce. Herein, we performed a systematic genomic analysis of 864 tet(X)-positive E. coli isolates from humans, animals and the environment around the world. These isolates were reported in 25 countries and isolated from 13 different hosts. China reported the most tet(X)-positive isolates (71.76 %), followed by Thailand (8.45 %) and Pakistan (5.9 %). Pigs (53.93 %), humans (17.41 %), and chickens (17.41 %) were determined to be important reservoirs of these isolates. The sequence types (STs) of E. coli were highly diverse, with the ST10 clone complex (Cplx) being the most prevalent clone. Correlation analysis revealed a positive association between the antibiotic resistance genes (ARGs) in ST10 E. coli and the presence of insertion sequences and plasmid replicons; however, we found no significant correlation between ARGs and virulence genes. Furthermore, the ST10 tet(X)-positive isolates from multiple sources displayed a high degree of genetic similarity (<200 single-nucleotide polymorphisms [SNPs]) to the mcr-1-positive but tet(X)-negative human-derived isolates, suggesting clonal transmission. The most prevalent tet(X) variant in the E. coli isolates was tet(X4), followed by tet(X6)-v. Genome-wide association study (GWAS) indicated that compared to tet(X4), tet(X6)-v harbored more significantly different resistance genes. Notably, certain tet(X)-positive E. coli isolates from different geographical locations or hosts shared a few SNPs (<200 SNPs), indicating cross-contamination. Therefore, continuous global surveillance of tet(X)-positive E. coli is imperative in the future.

Aberrant activation of TCL1A promotes stem cell expansion in clonal haematopoiesis.

Mutations in a diverse set of driver genes increase the fitness of haematopoietic stem cells (HSCs), leading to clonal haematopoiesis1. These lesions are precursors for blood cancers2-6, but the basis of their fitness advantage remains largely unknown, partly owing to a paucity of large cohorts in which the clonal expansion rate has been assessed by longitudinal sampling. Here, to circumvent this limitation, we developed a method to infer the expansion rate from data from a single time point. We applied this method to 5,071 people with clonal haematopoiesis. A genome-wide association study revealed that a common inherited polymorphism in the TCL1A promoter was associated with a slower expansion rate in clonal haematopoiesis overall, but the effect varied by driver gene. Those carrying this protective allele exhibited markedly reduced growth rates or prevalence of clones with driver mutations in TET2, ASXL1, SF3B1 and SRSF2, butthis effect was not seen inclones withdriver mutations in DNMT3A. TCL1A was not expressed in normal or DNMT3A-mutated HSCs, but the introduction of mutations in TET2 or ASXL1 led to the expression of TCL1A protein and the expansion of HSCs in vitro. The protective allele restricted TCL1A expression and expansion of mutant HSCs, as did experimentalknockdown of TCL1A expression. Forced expression of TCL1A promoted the expansion of human HSCs in vitro and mouse HSCs in vivo. Our results indicate that the fitness advantage of several commonly mutated driver genes in clonal haematopoiesis may be mediated by TCL1A activation.

ST7 Becomes One of the Most Common Staphylococcus aureus Clones After the COVID-19 Epidemic in the City of Wuhan, China.

Staphylococcus aureus (S. aureus) was able to rapidly evolve and adapt under the pressure of antibiotics, host immune and environmental change. After Corona Virus Disease 2019 (COVID-19) epidemic in Wuhan, China, a large number of disinfectants were used, which might result in rapid evolution of S. aureus. A total of 619 S. aureus isolates were collected from Zhongnan Hospital, Wuhan University from 2018 to 2021, including group BEFORE (309 strains collected before COVID-19 pandemic) and group AFTER (310 strains collected after COVID-19 pandemic), for comparing the changes of molecular epidemiology. The molecular characteristics of isolates were analyzed by Multi-locus sequence typing (MLST), spa, chromosomal cassette mec (SCCmec) typing, virulence genes were screened by the PCR, antibiotic susceptibility test was carried out by the VITEK system. Thirty-six sequence types (STs) belonging to 14 clone complexes (CCs) were identified. ST5 was the most prevalent clone in both groups, and ST7, ranking the sixth in group BEFORE, became the second dominant clone in group AFTER (6.5% vs 10.0%), whereas ST239 decreased from the seventh to the fourteenth (5.8% vs 1.9%). ST7 in group AFTER had a higher positive rate of virulence genes, including hlb, fnbB, seb, lukDE, sdrE and the proportion of ST7-t091 MRSA strains increased from 19.1% to 50% compared with group BEFORE. Though no significant difference of MRSA proportion was found between two groups, SCCmec type-III in group AFTER decreased (p<0.01). Though the rate of multidrug-resistance (MDR) decreased, the virulence genes hlb, hlg, fnbB, seb and pvl carrying rates were significantly elevated in MRSA strains of group AFTER. After COVID-19 pandemic, ST7 becomes one of the predominant S. aureus clones in Wuhan and the carrying rate of SCCmec and virulence genes is on the rise. Therefore, it is essential to strengthen the surveillance of ST7 S. aureus clone.

Phylogenetic analysis and virulence characteristics of methicillin-resistant Staphylococcus aureus ST764-SCCmec II: an emerging hypervirulent clone ST764-t1084 in China

ABSTRACT Previous studies have shown that the increased prevalent ST764 clone in China, Japan, and other Asian areas. However, the knowledge of the genetic features and virulence characteristics of methicillin-resistant Staphylococcus aureus (MRSA) ST764 in China is still limited. In this study, we identified 52 ST764-SCCmec type II isolates collected from five cities in China between 2014 and 2021. Whole genome sequencing showed that the most common staphylococcal protein A (spa) types of ST764 in China were t002 (55.78%) and t1084 (40.38%). Virulence assays showed that ST764-t1084 isolates had high haemolytic activity and α-toxin levels. Of the critical regulatory factors affecting α-toxin production, only the SaeRS was highly expressed in ST764-t1084 isolates. Mouse abscess model indicated that the virulence of ST764-t1084 isolates was comparable to that of S. aureus USA300-LAC famous for its hypervirulence. Interestingly, ST764-t002 isolates exhibited stronger biofilm formation and cell adhesion capacities than ST764-t1084 isolates. This seems to explain why ST764-t002 subclone has become more prevalent in China in recent years. Phylogenetic analysis suggested that all ST764 isolates from China in Clade III were closely related to KUN1163 (an isolate from Japan). Notably, genomic analysis revealed that the 52 ST764 isolates did not carry arginine catabolic mobile element (ACME), which differed from ST764 isolates in Japan. Additionally, most ST764 isolates (69.23%) harboured an obvious deletion of approximately 5 kb in the SCCmec II cassette region compared to KUN1163. Our findings shed light on the potential global transmission and genotypic as well as phenotypic characteristics of ST764 lineage.

Antimicrobial Resistance, Virulence, and Genetic Characterization of Methicillin-Resistant Staphylococcus aureus Recovered from Ready-to-Eat (RTE) Food in China: A New Challenge for Food Safety

Objective: The objective of the present study was to determine the prevalence, antimicrobial resistance, virulence profiles, and molecular characteristics of methicillin-resistant Staphylococcus aureus (MRSA) obtained from ready-to-eat (RTE) foods in China. Methods: Two hundred seventy-six RTE food-associated S. aureus isolates were collected from 25 provinces across China in 2018, then characterized by antimicrobial susceptibility testing, virulence factors detecting, multilocus sequence typing (MLST), spa typing, SCCmec typing and pulsed-field gel electrophoresis (PFGE). Results: Two hundred fifty isolates (90.6%) were resistant to at least one antimicrobial agent; 73 (26.4%) isolates were multi-drug resistant (MDR). Thirty MRSA isolates were identified, among which nine toxin genes (sea, seb, sec, sed, seh, selk, sell, selq, and tsst-1) were detected. Sixty percent (18/30) of the MRSA isolates harbored multiple toxin genes. Four virulence gene patterns were identified, with seb-selk-selq (30/30) being the most common pattern. Thirteen sequence types, as well as 13 spa and 4 SCCmec types were found among 30 MRSA isolates. The most prevalent MRSA lineages were CC59-t437-SCCmecIV/V (23.3% [7/30]), CC398-t011-SCCmecV (23.3% [7/30]), and CC1-t114-SCCmecIV (16.7% [5/30]). Conclusions: Our findings highlight the importance for the identification of prevalent clones, assessment of drug-resistance and virulence, and formulation of food safety measures for public health.

Molecular Epidemiology, Clinical Characteristics and Risk Factors for Bloodstream Infection of Multidrug-Resistant Klebsiella pneumoniae Infections in Pediatric Patients from Tianjin, China.

The data on pediatrics with Multidrug-Resistant (MDR) Klebsiella pneumoniae infections are scarce. This study aims to investigate the molecular epidemiology of MDR Klebsiella pneumoniae, detect the mechanism of drug resistance, and determine the clinical risk factors for carbapenem-resistant Klebsiella pneumonia (CRKP) bloodstream infections (BSIs) in a children's hospital. A total of 62 strains were collected from Tianjin Children's Hospital. Carba NP and polymerase chain reactions (PCR) were performed to detect MDR mechanisms. Multilocus sequence typing (MLST) was used for analyzing strain homology. Clinical data were collected and logistic regression was used for BSI risk factors. ST11 was the principal ST among the CRKP isolates clinically, accounting for 56.45% (35/62); there were also 57.14% (20/35) ST11 CRKP strains co-carrying bla NDM-5 and bla KPC-2, which were resistant to most of the tested antibiotics, being susceptible only to cotrimoxazole and tigecycline. The clinical data showed that 72.73% (40/55) of children with CRKP infection had serious underlying diseases; 20.00% (11/55) patients developed BSIs with the potential to cause multiple organ failure, shock and death. The logistic regression showed that the risk of BSIs caused by CRKP strain infections in children with hematological malignancies after chemotherapy was 7 times that of other children (95%Cl: 1.298-45.415, P=0.025). ST11 was the prevalent clone in our hospital. The emergence of ST11 CRKP co-carrying bla NDM-5 and bla KPC-2 should be a cause for alarm as they were resistant to most of the tested antibiotics. CRKP strain infections are mainly occurring in young immunocompromised patients and the chemotherapy for hematological malignancies is an independent risk factor for BSIs.

Genetic Diversity, Antibiotic Resistance, and Virulence Gene Features of Methicillin-Resistant Staphylococcus aureus Epidemics in Guiyang, Southwest China.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most common pathogens of community- and hospital-acquired infections, and its prevalence is increasing globally. Guiyang is the capital city of Guizhou Province, Southwest China; as the transport and tourism centre of Southwest China, Guizhou Province is bordered by Yunnan, Sichuan, Chongqing, and Guangxi Provinces. Although MRSA prevalence is increasing, little is known about its aspects in the area. The purpose of this study was to analyse MRSA molecular characteristics, antimicrobial resistance, and virulence genes in Guiyang. In total, 209 MRSA isolates from four hospitals (2019-2020) were collected and analysed by antimicrobial susceptibility testing and molecular classification by the MLST, spa, and SCCmec typing methods. Isolate antibiotic resistance rates were detected by a drug susceptibility assays. PCR amplification was used to detect the virulence gene-carrying status. Twenty-four STs, including 4 new STs (ST7346, ST7347, ST7348, and ST7247) and 3 new allelic mutations, were identified based on MLST. The major prevalent ST type and clone complex were ST59 (49.8%) and CC59 (62.7%), respectively. Spa type t437 (42.1%) and SCCmec IV (55.5%) were identified by spa and SCCmec typing methods as the most important types. Drug sensitivity data showed that the multidrug resistance rate was 79.0%. There were significant differences in multidrug resistance rates and virulence gene-carrying rates for seb, hla, hlb, cna and bap between ST59 and non-ST59 types. ST59-SCCmecIV-t437 is a major epidemic clone in Guiyang that should be monitored by local medical and health institutions. The situation differs from other adjacent or middle provinces of China, which may be due to the special geographical location of the region and the trend in antibiotic use or lifestyle. This study provides empirical evidence for local medical and health departments to prevent and control the spread of MRSA.

Molecular analysis of enteropathogenic Escherichia coli (EPEC) isolates from healthy food-producing animals and humans with diarrhoea.

Enteropathogenic Escherichia coli (EPEC) is a pathogen associated with acute diarrhoea in humans. To determine whether EPEC isolated from healthy food-producing animals possesses the same virulence gene repertoire as EPEC isolated from human with diarrhoea, we compared six typical EPEC (tEPEC) and 20 atypical EPEC (aEPEC) from humans with diarrhoea and 42 aEPEC from healthy animals (swine, sheep and buffaloes), using pulsed-field gel electrophoresis (PFGE), virulence markers, serotyping and subtyping of eae and tir genes. We found that human and animal isolates shared virulence genes, including nleB, nleE and nleF, which were associated with human diarrhoea. Serogroups and serotypes identified in isolates of food-producing animals such as O26:H11, O128:H2, O76:H7, O103, O108, O111 and O145, have previously been implicated in human disease. The subtypes eae and tir were also shared between human and animal isolates, being eae-γ1 and eae-β1 the most prevalent in both groups, while the most common tir subtypes were α and β. Despite PFGE analysis demonstrating that EPEC strains are heterogeneous and there was no prevalent clone identified, EPEC isolated from humans and food-producing animals shared some characteristics, such as virulence genes associated with human diarrhoea, indicating that food-producing animals could play a role as reservoirs for those genes.

Epidemiology of carbapenem-resistant Klebsiella pneumoniae ST15 of producing KPC-2, SHV-106 and CTX-M-15 in Anhui, China

Background:It is well known that carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a more problematic public health issue due to its widespread spread worldwide. In China, ST11-type CRKP is the most prevalent CRKP, but ST15-type CRKP, a recently prevalent high-risk clone, has emerged widely throughout China, posing a serious public health risk. Therefore, we conducted an epidemiological of an outbreak of ST15 CRKP of producing CTX-M-15, KPC-2 and SHV-106 in a tertiary hospital in Anhui, China, to Understanding the potential risks of the current STT15 CRKP outbreak.Results:From July 2021 to December 2021, 13 ST15 CRKP isolates were identified by collecting non-repeated clinical multidrug-resistant isolates, with all capsular typing of serotype KL19. All ST15 CRKP isolates were resistant to cephalosporins, carbapenems and quinolones, but were sensitive to amikacin, tigecycline and polymyxin B. In addition, isolates carried blaSHV−106 (100%), blaKPC−2 (69%), blaCTX−M−15 (69%), blaTEM−1B (69%), blaOXA−1 (62%) and blaLAP−2 (8%), as well as iron chelators (iutA, ybt, fyuA, ent, fepA, irp1, irp2, 100%) were detected. In phenotyping experiments, all ST15 CRKP exhibited lower growth rates than NTUH-K2044, and all ST15 CRKP did not exhibit mucoviscositty characteristics. However, in the Galleria mellonella infection model, isolates 21081212, 21081241 and 21091216 were more lethal than the hypervirulent isolates NTUH-K2044. Sequencing results showed that the genetic environment surrounding the genes blaSHV−106, blaKPC−2, blaCTX−M−15, blaOXA−1 and blaTEM−1B were all identical in the ST15 CRKP isolates. Phylogenetic analysis showed that 13 ST15 CRKP isolates were divided into three subgroups, and when placed in global analysis, 10 of them were highly homologous to isolates from Jiangsu, two were highly homologous to isolates from Zhejiang, and one was homologous to an isolate from an unlabelled region.Conclusion:Our research shows that ST15 CRKP, which carries multiple β-lactamases genes and siderophores-encoding genes, may be evolving to hypervirulence and may have spread widely in localised areas. Therefore, environmental surveillance and clinical infection control in hospitals should be strengthened to prevent further spread of ST15 CRKP.

Temporo-spatial variations in resistance determinants and clonality of Acinetobacter baumannii and Pseudomonas aeruginosa strains from Romanian hospitals and wastewaters

BackgroundRomania is one of the European countries reporting very high antimicrobial resistance (AMR) rates and consumption of antimicrobials. We aimed to characterize the AMR profiles and clonality of 304 multi-drug resistant (MDR) Acinetobacter baumannii (Ab) and Pseudomonas aeruginosa (Pa) strains isolated during two consecutive years (2018 and 2019) from hospital settings, hospital collecting sewage tanks and the receiving wastewater treatment plants (WWTPs) located in the main geographical regions of Romania.MethodsThe strains were isolated on chromogenic media and identified by MALDI-TOF-MS. Antibiotic susceptibility testing and confirmation of ESBL- and CP- producing phenotypes and genotypes were performed. The genetic characterization also included horizontal gene transfer experiments, whole-genome sequencing (WGS), assembling, annotation and characterization.ResultsBoth clinical and aquatic isolates exhibited high MDR rates, especially the Ab strains isolated from nosocomial infections and hospital effluents. The phenotypic resistance profiles and MDR rates have largely varied by sampling point and geographic location. The highest MDR rates in the aquatic isolates were recorded in Galați WWTP, followed by Bucharest. The Ab strains harbored mostly blaOXA-23, blaOXA-24, blaSHV, blaTEM and blaGES, while Pa strains blaIMP, blaVIM, blaNDM, blaVEB, blaGES and blaTEM, with high variations depending on the geographical zone and the sampling point. The WGS analysis revealed the presence of antibiotic resistance genes (ARGs) to other antibiotic classes, such as aminoglycosides, tetracyclines, sulphonamides, fosfomycin, phenicols, trimethoprim-sulfamethoxazole as well as class 1 integrons. The molecular analyses highlighted: (i) The presence of epidemic clones such as ST2 for Ab and ST233 and ST357 for Pa; (ii) The relatedness between clinical and hospital wastewater strains and (iii) The possible dissemination of clinical Ab belonging to ST2 (also proved in the conjugation assays for blaOXA-23 or blaOXA-72 genes), ST79 and ST492 and of Pa strains belonging to ST357, ST640 and ST621 in the wastewaters.ConclusionOur study reveals the presence of CP-producing Ab and Pa in all sampling points and the clonal dissemination of clinical Ab ST2 strains in the wastewaters. The prevalent clones were correlated with the presence of class 1 integrons, suggesting that these isolates could be a significant reservoir of ARGs, being able to persist in the environment.

Molecular Epidemiology of Multidrug-Resistant Pseudomonas aeruginosa Acquired in a Spanish Intensive Care Unit: Using Diverse Typing Methods to Identify Clonal Types.

The increasing number of infections from multidrug-resistant P. aeruginosa (MDRPA) has compromised the selection of appropriate treatment in critically ill patients. Recent investigations have shown the existence of MDRPA global clones that have been disseminated in hospitals worldwide. We aimed to describe the molecular epidemiology and genetic diversity of the MDRPA acquired by Intensive Care Units (ICU) patients in our hospital. We used phenotypic methods to define the MDRPA and molecular methods were used to illustrate the presence of carbapenemase encoding genes. To characterize the MDRPA isolates, we used MALDI-TOF biomarker peaks, O-antigen serotyping, and multi-locus sequence typing analyses. Our data show that the most widely distributed MDRPA clone in our ICU unit was the ST175 strain. These isolates were further investigated by the whole-genome sequencing technique to determine the resistome profile and phylogenetic relationships, which showed, as previously described, that the MDR profile was due to the intrinsic resistance mechanisms and not the carbapenemase encoding genes. In addition, this study suggests that the combination of environmental focus and cross-transmission are responsible for the spread of MDRPA clones within our ICU unit. Serotyping and MALDI-TOF analyses are useful tools for the early detection of the most prevalent MDRPA clones in our hospital. Using these methods, semi-directed treatments can be introduced at earlier stages and healthcare professionals can actively search for environmental foci as possible sources of outbreaks.

The Gastrointestinal Load of Carbapenem-Resistant Enterobacteriacea Is Associated With the Transition From Colonization to Infection by Klebsiella pneumoniae Isolates Harboring the blaKPC Gene.

BackgroundHealthcare-associated infections by carbapenem-resistant Klebsiella pneumoniae are difficult to control. Virulence and antibiotic resistance genes contribute to infection, but the mechanisms associated with the transition from colonization to infection remain unclear.ObjectiveWe investigated the transition from carriage to infection by K. pneumoniae isolates carrying the K. pneumoniae carbapenemase–encoding gene bla KPC (KpKPC).MethodsKpKPC isolates detected within a 10-year period in a single tertiary-care hospital were characterized by pulsed-field gel electrophoresis (PFGE), multilocus sequencing typing, capsular lipopolysaccharide and polysaccharide typing, antimicrobial susceptibility profiles, and the presence of virulence genes. The gastrointestinal load of carbapenem-resistant Enterobacteriaceae and of bla KPC-carrying bacteria was estimated by relative quantification in rectal swabs. Results were evaluated as contributors to the progression from carriage to infection.ResultsNo PGFE type; ST-, K-, or O-serotypes; antimicrobial susceptibility profiles; or the presence of virulence markers, such yersiniabactin and colibactin, were associated with carriage or infection, with ST437 and ST11 being the most prevalent clones. Admission to intensive and semi-intensive care units was a risk factor for the development of infections (OR 2.79, 95% CI 1.375 to 5.687, P=0.005), but higher intestinal loads of carbapenem-resistant Enterobacteriaceae or of bla KPC-carrying bacteria were the only factors associated with the transition from colonization to infection in this cohort (OR 8.601, 95% CI 2.44 to 30.352, P<0.001).ConclusionThe presence of resistance and virulence mechanisms were not associated with progression from colonization to infection, while intestinal colonization by carbapenem-resistant Enterobacteriacea and, more specifically, the load of gastrointestinal carriage emerged as an important determinant of infection.

The Correlation Between Biofilm-Forming Ability of Community-Acquired Methicillin-Resistant Staphylococcus aureus Isolated from the Respiratory Tract and Clinical Characteristics in Children.

ObjectiveThis study aimed to investigate the biofilm-forming ability, molecular typing, and antimicrobial resistance of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) strains isolated from the respiratory tract of children and their correlation with clinical characteristics.MethodsAll CA-MRSA strains were isolated from hospitalized children, and their presentation, molecular typing, antimicrobial susceptibility, and biofilm formation were investigated. The clinical characteristics were compared between the strong and weak biofilm producer groups.ResultsFifty-three CA-MRSA strains were isolated from the respiratory samples of 53 children, with nearly half of them being young infants (0–12 months). Approximately, 88.7% (47/53) of the isolates were resistant to four or more antibiotics, mainly β-lactam antibiotics, lincosamides, and macrolides. Twelve sequence types (STs) and 20 subtypes of staphylococcal protein A (spa) typing were identified, with ST59-t437 (39.6%, 21/53) as the predominant subtype. All strains showed the ability to form biofilms. When compared to children with weak biofilm-forming CA-MRSA strains, those with strong biofilm-forming strains had higher proportions of lower respiratory tract infections (LRTI) (88.5% vs 59.3%), obvious cough symptoms (84.6% vs 51.9%), and severe chest imaging manifestations (76.9% vs 37.0%). Furthermore, a strong biofilm-forming ability significantly increased the risk of prolonged cough in children with LRTI (44.4% vs 14.3%), and a positive correlation between the duration of cough and the extent of biofilm formation was observed. Medical history investigation revealed that the strong biofilm-forming group had a much higher percentage of macrolides intake than the weak biofilm-forming group in the last month before admission (61.5% vs 14.8%).ConclusionST59-t437 was the most prevalent clone in CA-MRSA respiratory isolates among the hospitalized children. All CA-MRSA strains formed biofilms. The stronger the biofilm-forming ability, the more serious and prolonged were the respiratory symptoms.

Genomic Characterization of Mobile Genetic Elements Associated With Carbapenem Resistance of Acinetobacter baumannii From India.

With the excessive genome plasticity, Acinetobacter baumannii can acquire and disseminate antimicrobial resistance (AMR) genes often associated with mobile genetic elements (MGEs). Analyzing the genetic environment of resistance genes often provides valuable information on the origin, emergence, evolution, and spread of resistance. Thus, we characterized the genomic features of some clinical isolates of carbapenem-resistant A. baumannii (CRAb) to understand the role of diverse MGEs and their genetic context responsible for disseminating carbapenem resistance genes. For this, 17 clinical isolates of A. baumannii obtained from multiple hospitals in India between 2018 and 2019 were analyzed. AMR determinants, the genetic context of resistance genes, and molecular epidemiology were studied using whole-genome sequencing. This study observed an increased prevalence of blaOXA–23 followed by dual carbapenemases, blaOXA–23, and blaNDM. This study identified three novel Oxford MLST sequence types. The majority of the isolates belonged to the dominant clone, IC2, followed by less prevalent clones such as IC7 and IC8. This study identified variations of AbaR4 and AbGRI belonging to the IC2 lineage. To the best of our knowledge, this is the first study that provides comprehensive profiling of resistance islands, their related MGEs, acquired AMR genes, and the distribution of clonal lineages of CRAb from India.

Vibrio parahaemolyticus O10:K4: An Emergent Serotype with Pandemic Virulence Traits as Predominant Clone Detected by Whole-Genome Sequence Analysis - Beijing Municipality, China, 2021.

IntroductionVibrio parahaemolyticus (V. parahaemolyticus) is a common foodborne pathogen which causes gastroenteritis in humans, especially the O3:K6 pandemic clone which is still a prominent serotype in Beijing, China. In this study, we observed a novel serotype O10:K4 isolated from clinical diarrhea cases, which became the most prevalent clone in 2021. Methods73 clinical isolates were collected through sentinel hospitals’ surveillance in 2021. Serum agglutination testing and antimicrobial susceptibility testing were conducted. Whole genome sequencing was applied to characterize 73 V. parahaemolyticus strains and complete phylogenetic analysis. ResultsSeven serotypes were identified among 73 strains. O10:K4 was the most common serotype (83.6%), followed by O2:KUT, O4:KUT, and O1:KUT. Multilocus sequence typing divided the 73 isolates into 10 sequence types (STs) with ST3 as the most prevalent, which covered all O10:K4 strains. Most isolates were sensitive to common antimicrobial agents apart from colistin. All the O10:K4 isolates were positive for the thermostable direct hemolysin gene, toxRS/new, andorf8, and negative for the TDH-related hemolysin gene. The whole genome sequencing-single nucleotide polymorphism phylogenetic analysis revealed O10:K4 strains formed a main genetic lineage, which was genetically distinct from other serotypes. We also demonstrated the presence of two type III secretion system genes (T3SS1 and T3SS2) and β lactamase resistance gene blaCARB-22 in all O10:K4 strains. ConclusionsThe study confirmed the emergence of V. parahaemolyticus O10:K4 possessing virulence factors similar to the O3:K6 pandemic clone, which may have enabled them to become prevalent in Beijing, China.

Molecular Epidemiological Characteristics of Mycobacterium abscessus Complex Derived from Non-Cystic Fibrosis Patients in Japan and Taiwan.

ABSTRACTMycobacterium abscessus complex (MABC) is a group of emerging, highly antimicrobial-resistant non-tuberculous mycobacteria. Specific MABC clones are spreading globally in patients with cystic fibrosis (CF); however, associated genomic epidemiology is lacking in East Asia, with very few patients with CF. Here, we investigated MABC populations derived from non-CF patients in Japan and Taiwan. Analysis of whole-genome sequencing data of 220 MABC isolates revealed that 112, 105, and 3 were M. abscessus subsp. abscessus (ABS), M. abscessus subsp. massiliense (MAS), and M. abscessus subsp. bolletii (BOL), respectively. Moreover, >50% of ABS and >70% of MAS were related to four predominant clones in the region. Known mutations conferring macrolide resistance were rare (1.4%) and were not enriched in the predominant clones. Conversely, the macrolide-susceptible erm(41) T28C mutation was significantly enriched in one predominant ABS clone. The most predominant ABS clone was genetically related to the previously described dominant circulating clone (DCC)1 in patients with CF, whereas no isolates were related to DCC2; isolates related to DCC3 were not necessarily predominant in our sample set. We found that the erm(41) T28C mutants spread globally, and some of them reacquired the functional erm(41) gene through both point mutation and recombination. This study revealed predominant MABC clones in Japan and Taiwan and their relationship with the globally superadding clones in the patient community with CF. Our study provides insights into the genetic characteristics of globally dominant and area-specific strains isolated from patients with or without CF and differences between globally spread and regionally specific strains.IMPORTANCE Members of Mycobacterium abscessus complex (MABC) are frequently isolated from patients. Studies have reported that predominant clones of MABC (known as dominant circulating clones; DCCs) are distributed worldwide and transmitted from humans to humans in patients with cystic fibrosis (CF). However, associated genomic epidemiology has not yet been conducted in East Asia, including Japan and Taiwan, where there are only a few patients with CF. Using whole-genome sequencing data derived from non-CF patients in Japan and Taiwan, we revealed prevalent clones and the incidence of macrolide resistance-associated mutations in the MABC population in this region. We also clarified the associations between these predominant clones and DCCs in the global CF patient community. Our results would assist further studies in elucidating the genetic characteristics of strains isolated from patients with or without CF, the differences between globally spread and regionally specific strains, and the adaptive evolution of MABC within the host.