Antimicrobial Resistance Characteristics Research Articles

Antimicrobial resistance and genomic characteristics of Salmonella from broilers in Shandong Province

IntroductionThe emergence of multidrug-resistant (MDR) strains of Salmonella, which is a genus of important zoonotic pathogens, has aroused great public health concern worldwide.MethodsIn this study, 167 strains of Salmonella were isolated from 947 samples from broiler farms, slaughterhouses, and markets in Shandong Province. Antibiotic sensitivity testing was performed, and 70 strains of Salmonella were screened out by whole-genome sequencing (WGS) to evaluate serotypes, antimicrobial resistance genes (ARGs), the prevalence of class 1 integrons, the plasmid carriage rate, and phylogenetic characteristics and for multilocus sequence typing (MLST).ResultsThe results showed that the 167 isolates showed the highest resistance to ampicillin (AMP, 87.4%), sulfamethoxazole (SF, 87.4%), compound sulfamethoxazole (SXT, 81.4%), nalidixic acid (NAL, 80.2%), and amoxicillin/clavulanic acid (A/C, 77.8%). All the strains were sensitive to meropenem (MEM), and 91.0% of the isolates were MDR strains. We screened a total of 45 ARGs, with the highest detection rate observed for the tetracycline (TET) resistance gene tet (A) (81.4%). A total of 21 types of plasmid replicons were detected in Salmonella, of which IncX1 was the most common (74.3%), and 62.9% of the isolates carried a class 1 integron. In addition, a total of 11 different serotypes were detected, with S. enteritidis as the predominant serovar., followed by S. infantis and S. Newport. Twelve different sequence types (STs) were detected, among which ST11 was the main type. There was a strong correspondence between serotypes and STs. We also found that S. Indiana and S. Kentucky had extremely high rates of resistance to ciprofloxacin (CIP) and third-generation cephalosporins. System-wide genome analysis showed the occurrence of long-distance transmission across fields.ConclusionIn conclusion, the detection of multidrug resistance and isolates carrying multidrug resistance genes is the main problem, and emergency strategies should be implemented to address this issue.

Incidence of co-resistance to antibiotics and chlorine in bacterial biofilm of hospital water systems: Insights into the risk of nosocomial infections

The presence of biofilms in drinking water distribution systems (DWDS) in healthcare settings poses a considerable risk to the biological security of water, particularly when the biofilm bacteria demonstrate antimicrobial resistance characteristics. This study aimed to investigate the occurrence of antibiotic-resistant bacteria (ARB) in biofilms within DWDS of hospitals. The chlorine resistance of the isolated ARB was analyzed, and then chlorine-resistant bacteria (CRB) were identified using molecular methods. Additionally, the presence of several antibiotic resistance genes (ARGs) was monitored in the isolated ARB. Out of the 41 biofilm samples collected from hospitals, ARB were detected in 32 (78%) of the samples. A total of 109 colonies of ARB were isolated from DWDS of hospitals, with β-lactam resistant bacteria, including ceftazidime-resistant and ampicillin-resistant bacteria, being the most frequently isolated ARB. Analyzing of ARGs revealed the highest detection of aac6, followed by sul1 gene. However, the β-lactamase genes blaCTX-M and blaTEM were not identified in the ARB, suggesting the presence of other β-lactamase genes not included in the tested panel. Exposure of ARB to free chlorine at a concentration of 0.5 mg/l showed that 64% of the isolates were CRB. However, increasing the chlorine concentration to 4 mg/l decreased the high fraction of ARB (91%). The domi‌‌nant CRB identified were Sphingomonas, Brevundimonas, Stenotrophomonas, Bacillus and Staphylococcus with Bacillus exhibiting the highest frequency. The results highlight the potential risk of biofilm formation in the DWDS of hospitals, leading to the dissemination of ARB in hospital environments, which is a great concern for the health of hospitalized patients, especially vulnerable individuals. Surveillance of antimicrobial resistance in DWDS of hospitals can provide valuable insights for shaping antimicrobial use policies and practices that ensure their efficacy.

Distribution and association of antimicrobial resistance and virulence characteristics in Enterococcus spp. isolates from captive Asian elephants in China.

Enterococcus spp., as an opportunistic pathogen, are widely distributed in the environment and the gastrointestinal tracts of both humans and animals. Captive Asian elephants, popular animals at tourist attractions, have frequent contact with humans. However, there is limited information on whether captive Asian elephants can serve as a reservoir of antimicrobial resistance (AMR). The aim of this study was to characterize AMR, antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), gelatinase activity, hemolysis activity, and biofilm formation of Enterococcus spp. isolated from captive Asian elephants, and to analyze the potential correlations among these factors. A total of 62 Enterococcus spp. strains were isolated from fecal samples of captive Asian elephants, comprising 17 Enterococcus hirae (27.4%), 12 Enterococcus faecalis (19.4%), 8 Enterococcus faecium (12.9%), 7 Enterococcus avium (11.3%), 7 Enterococcus mundtii (11.3%), and 11 other Enterococcus spp. (17.7%). Isolates exhibited high resistance to rifampin (51.6%) and streptomycin (37.1%). 50% of Enterococcus spp. isolates exhibited multidrug resistance (MDR), with all E. faecium strains demonstrating MDR. Additionally, nine ARGs were identified, with tet(M) (51.6%), erm(B) (24.2%), and cfr (21.0%) showing relatively higher detection rates. Biofilm formation, gelatinase activity, and α-hemolysin activity were observed in 79.0, 24.2, and 14.5% of the isolates, respectively. A total of 18 VAGs were detected, with gelE being the most prevalent (69.4%). Correlation analysis revealed 229 significant positive correlations and 12 significant negative correlations. The strongest intra-group correlations were observed among VAGs. Notably, we found that vancomycin resistance showed a significant positive correlation with ciprofloxacin resistance, cfr, and gelatinase activity, respectively. In conclusion, captive Asian elephants could serve as significant reservoirs for the dissemination of AMR to humans.

Molecular Characterisation of Antimicrobial Resistance in E. coli Isolates from Piglets in the West Region of Romania.

Antibiotics are widely used for prophylaxis and therapy, reducing morbidity and mortality produced by bacterial pathogensin pigs, including infections caused by Escherichia coli. The aim of this study was to characterise antibiotic resistance phenotypes and genotypes in E. coli isolates in pigs in West Romanian grower farms. Differential phenotypic susceptibility profiles and the contribution of resistance genes to phenotypic expression of susceptibility or resistance were evaluated. A total of 76 E. coli isolates were identified and confirmed by the MicroScan Walk Away System. The occurrence of four resistance genes, ampC, blaZ, blaTEM and tetK in strains resistant to 13 antibiotics was assessed. Of the E. coli isolates, 0% showed resistance to meropenem, 3.9% to tigecycline and 10.5% to piperacillin/tazobactam, whereas, in contrast, 100% were resistant to ampicillin and mezlocillin, 76.31% to piperacillin and 59.3% to tetracycline. The prevalence of resistance genes in resistant isolates detected by q-PCR analysis was 97.0% for ampC, 96% for blaZ, 32.9% for blaTEM and 58.8% for tetK. Penetrance (the proportion of individuals carrying a particular variant of a gene that also expresses an associated trait) was 50% for ampC (32% for amoxicillin/clavulanate, 62% for cefazolin, 32% for cefepime, 100% for cefotaxime, 56% for cefuroxime and 99% for ampicillin), 65% for blaZ (32% for amoxicillin/clavulanate and 99% for ampicillin), 51% for blaTEM (81% for piperacillin) and 44% for the tetK gene (83% for tetracycline). The result of phenotypic antibiotic resistance testing may indicate the presence of plasmid-borne resistance, with a diagnostic odds ratio of a positive phenotypic resistance for tetK being 4.52. As a management decision, the maximum penetrance admitted for using a specific antibiotic for E. coli infections in pigs is recommended to be less than 20%.

The characterization and correlation between the phenotypic and genotypic resistance of Campylobacter spp. isolates from commercial broilers and native chickens in the south of Thailand

ABSTRACT Chicken is a major reservoir and source of human infections from zoonotic Campylobacter. In southern Thailand, chicken is the most popular meat consumed; however, little is known about the antimicrobial resistance (AMR) of Campylobacter spp. in chicken production systems. We aimed to investigate the prevalence and characteristics of AMR in Campylobacter isolates from commercial broiler and native chicken farms in southern Thailand. A total of 286 Campylobacter isolates (adjusted prevalence: 60.3%, SE ± 0.01) were recovered, of which 268 were identified as Campylobacter jejuni and 18 as Campylobacter coli. The adjusted prevalence of resistance was highest for nalidixic acid (98.6%), followed by ciprofloxacin (97.2%), enrofloxacin (96.4%), tetracycline (74.6%), tylosin (38.3%), and erythromycin (10.6%). Commercial broilers had resistance levels 7–11% higher to quinolones and 35–47% lower to macrolides and tetracycline (all P ≤ 0.025) compared to native chickens. Genotypic resistance analyses revealed high prevalence rates (>86%) for gyrA mutant, efflux pump CmeABC, and point mutation A2075G in the 23S rRNA gene. High homogeneity was observed among isolates within study farms. Commercial broilers exhibited higher homogeneity in AMR patterns than native chickens. The best agreement was observed between tetracycline resistance and tet(O) genes (Kappa: k = 0.811, P < 0.001), while the fair agreement was found for quinolone resistance and gyrA mutant genes (k = 0.260–0.271, P < 0.001). No association was detected between macrolide resistance and point mutations in the 23S rRNA gene. These findings fill knowledge gaps on AMR in Campylobacter in Thailand, emphasizing the need for targeted AMR mitigation strategies in both commercial broilers and native chickens. RESEARCH HIGHLIGHTS High Campylobacter prevalence in chickens; C. jejuni more prevalent than C. coli. Susceptibility to macrolides but resistance to quinolones/tetracyclines in isolates. Homogeneous resistance patterns within farms; higher in broilers than in native birds. Partial association between phenotypic and genotypic resistance among isolates.

Emergence of ST1193 Clone in Maternal and Neonatal ESBL-Producing E. coli Isolates.

The emerging epidemic of extended-spectrum β-lactamase-producing E. coli (ESBL-EC) is a global public health crisis. ESBL-EC infections are increasing worldwide and contribute to morbidity and mortality among newborn infants. However, the antimicrobial resistance characteristics and clonal transmission of maternal and neonatal ESBL-EC isolates need to be further deciphered. We performed phenotypic and genotypic characterization of 33 ESBL-EC isolates from pregnant women and newborn during 2019-2020. Minimum inhibitory concentrations of 17 antimicrobial agents showed that all isolates were multidrug-resistant (MDR) and had a resistance rate of 100% to ampicillin, and mild resistance to florfenicol, gentamicin, ceftazidime, and amoxicillin-clavulanate. Additionally, imipenem, meropenem, polymyxin, and tigecycline exhibited good activity against the tested ESBL-EC isolates with low MIC50 (0.06-1 μg/mL) and MIC90 (0.06-1 μg/mL). Whole genome sequencing indicated that ESBL-EC isolates contained diverse antimicrobial resistant genes (blaCTX-M, blaTEM, blaSHV, tetA, etc.) and toxin genes (ompA, csg, fimH, hybtA, etc.). blaCTX-M genes were the main ESBL genotype. ST1193 (18.2%) was the second most abundant ST among the ESBL-EC isolates (ST131 was the most common, with 30.3%), and this is the first report of its mother-to-infant colonization transmission in China. These findings revealed the occurrence of high-risk ST1193 clone among ESBL-EC isolates from pregnant women and newborn colonization in China. Further national or regional multicenter studies are needed to assess the dissemination and evolution of ESBL-EC ST1193 clone as a nosocomial pathogen in China.

Molecular Characterization Of Antimicrobial Resistance In Edwardsiella Tarda Isolated From Diseased Tilapia Fish In Egypt

Molecular Characterization Of Antimicrobial Resistance In Edwardsiella Tarda Isolated From Diseased Tilapia Fish In Egypt

The occurrence and contamination of optrA-positive methicillin-resistant Staphylococcus aureus from duck farms in Guangdong, China

Staphylococcus aureus, especially methicillin-resistant S. aureus (MRSA), is an important zoonotic microorganism that increasingly causes public health concern worldwide. The objective of this study was to determine the prevalence and transmission of S. aureus in duck farms and evaluate its antimicrobial resistance and genetic characteristics. The samples associated with ducks, feeders, and the environment were collected on 14 duck farms from four areas in Guangdong, China, from 2020 to 2021. All isolates were subjected to antimicrobial susceptibility testing. A comprehensive epidemiological survey of S. aureus was conducted by S. aureus protein A typing and whole-genome sequencing. A total of 560 samples were collected. The prevalence rate of MRSA among ducks (8.1%, 11 of 135) was higher compared with that in environmental samples. OptrA-positive ST398-t034 MRSA were first detected from duck farms in China. A total of 79.3% (34 of 46) S. aureus isolates showed multidrug-resistant phenotypes. Notably, some isolates carried multidrug-resistant genes encoding macrolide-lincosamide-streptogramin B, pleuromutilin-pleuromutilin-streptogramin A, and oxazolidinone. Analysis of the virulence genes revealed that the MRSA isolates carried genes encoding gamma-hemolysin, enterotoxin, and leukocidin. ST9-t899 is a primary clonal lineage among duck- and environment-associated MRSA. Single-nucleotide polymorphism analysis showed the potential contamination relationship of optrA-positive ST2308 MRSA isolates carrying the gamma-hemolysin genes and the leukocidin virulence genes between airborne dust and sick ducks. The contamination of MRSA, especially optrA-positive MRSA, between food animals and the environment is a growing public health concern worldwide. Based on One Health principles, continuous surveillance of MRSA is urgently needed.

Prevalence and Antimicrobial-Resistant Features of Shigella Species in East Africa from 2015-2022: A Systematic Review and Meta-Analysis.

Shigellosis is the most common cause of epidemic dysentery found worldwide, particularly in developing countries, where it causes infant diarrhea and mortality. The prevalence of Shigella species resistant to commonly used antimicrobial drugs has steadily increased. The purpose of this review is to describe the prevalence and antimicrobial resistance (AMR) characteristics of Shigella species in East Africa between 2015 and 2022. Studies were identified using a computerized search of Medline/PubMed, Google Scholar, and Web of Science databases, with a detailed search strategy and cross-checking of reference lists for studies published between 2015 and 2022. Articles presenting data on prevalence and AMR, accessibility of the full-length article, and publication dates between 2015 and 2022 were the eligibility criteria for inclusion in the review. Original research reports written in English were considered. The heterogeneities of the studies were examined, and a meta-analysis was performed to estimate the pooled prevalence and AMR using a random effects model. The pooled prevalence of Shigella species in East Africa was 6.2% (95% CI -0.20-12.60), according to an analysis of 22 studies. Shigella species prevalence was 4.0% in Ethiopia, 14.6% in Kenya, 0.7% in Sudan, 5.2% in South Sudan, and 20.6% in Somalia. The association of Shigella infection significantly varied among the countries (p = 0.01). Among the antibiotics tested, most Shigella isolates were susceptible to ciprofloxacin, norfloxacin, nalidixic acid, and ceftriaxone. Despite the fact that the reports varied in study sites and time, Shigella species were resistant to tetracycline, ampicillin, amoxicillin, chloramphenicol, and co-trimoxazole. The pooled estimate indicates high burden of Shigella infection in East Africa, as well as a high proportion of drug resistance pattern to tetracycline, ampicillin, chloramphenicol, and amoxicillin. Therefore, initiating and scale-up of performing drug susceptibility test for each shigellosis case need to be considered and strengthened.

Arterial leg ulcers-Bacterial patterns, antimicrobial resistance and clinical characteristics, a retrospective single-centre cohort, 2012-2021.

Severe wound infections in patients with peripheral artery disease (PAD) are common, potentially life- and limb-threatening, and difficult to treat. Evidence on patients with infected leg ulcers in PAD is scarce. This study aims to provide insight into the microbiological patterns and antimicrobial resistance (AMR) of specific pathogens in patients with arterial leg ulcers. In this retrospective, consecutive, single-centre study 16,553 patients underwent an endovascular revascularization procedure between 2012 and 2021. Of these, 1,142 patients had PAD Rutherford category 5 or 6 with infected leg ulcers. Logistic regression was used to identify risk factors for Staphylococcus aureus-associated infections. A total of 3,431 bacterial isolates were detected, of which 2,335 (68.1%) bacterial isolates were gram-positive and 1,096 (31.9%) were gram-negative species. The most prevalent bacteria were S. aureus (18.6%), Enterococcus faecalis (9.1%) and S. epidermidis (7.8%). Pseudomonas aeruginosa (5.6%), Proteus mirabilis (3.7%) and Escherichia coli (3.4%). The resistance of S. aureus isolates to clindamycin was 11.0%. Resistance to oxacillin was rare (1.5%). P. aeruginosa is frequently resistant to ciprofloxacin (14.4%) whilst intrinsically resistant to trimethoprim/sulfamethoxazole. P. mirabilis and E. coli were frequently resistant to both ciprofloxacin (7.3; 20.7%) and trimethoprim/sulfamethoxazole (24.6; 22.6%), respectively. Resistance to amoxicillin/clavulanic acid was high among E. coli isolates (36.8%). Multi-drug resistance (MDR) was rare among S. aureus and P. aeruginosa isolates. In contrast, the proportion of MDR was high in E. coli isolates. End-stage renal disease was independently positively associated with S. aureus identification (p = .042). S. aureus was the most common pathogen in arterial leg ulcers with end-stage renal disease being an independent risk factor. Clindamycin resistance was common, making empirical therapy likely to fail. Isolated E. coli species had a high proportion of MDR.

Molecular epidemiological characterization of hypervirulent carbapenem-resistant Klebsiella pneumoniae in a hospital in Henan Province from 2020 to 2022

Objective: The study investigated the clinical distribution, antimicrobial resistance and epidemiologic characteristics of hypervirulent Carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) in a hospital in Henan Province to provide a scientific basis for antibiotic use and nosocomial infection prevention and control. Methods: A retrospective analysis of the clinical data from the cases was carried out in this study. Clinical data of patients infected with the CRKP strain isolated from the clinical microbiology laboratory of Henan Provincial Hospital of Traditional Chinese Medicine from January 2020 to December 2022 were retrospectively analyzed. A string test, virulence gene screening, serum killing, and a G. mellonella infection model were used to screen hv-CRKP isolates. The clinical characteristics of hv-CRKP and the drug resistance rate of hv-CRKP to twenty-five antibiotics were analyzed using WHONET 5.6. Carbapenemase phenotypic characterization of the hv-CRKP was performed by colloidal gold immunochromatographic assay, and Carbapenemase genotyping, multi-locus sequence typing (MLST) and capsular serotyping of hv-CRKP isolates were performed by PCR and Sanger sequencing. Results: A total of non-duplicate 264 CRKP clinical isolates were detected in the hospital from 2020 to 2022, and 23 hv-CRKP isolates were detected, so the corresponding detection rate of hv-CRKP was 8.71% (23/264). The hv-CRKP isolates in this study were mainly from the intensive care unit (10/23) and neurosurgery department (8/23), and the main sources of hv-CRKP isolates were sputum (10/23) and bronchoalveolar lavage fluid (6/23). The hv-CRKP isolates in this study were highly resistant to β-lactam antibiotics, fluoroquinolones and aminoglycosides, and were only susceptible to colistin, tigecycline and ceftazidime/avibactam. The detection rate of the blaKPC-2 among 23 hv-CRKP isolates was 91.30% (21/23) and none of the class B and class D carbapenemases were detected. Results of MLST and capsular serotypes showed that ST11 type hv-CRKP was the dominant strain in the hospital, accounting for 56.52% (13/23), and K64 (9/13) and KL47 (4/13) were the major capsular serotypes. Conclusion: The hv-CRKP isolates from the hospital are mainly from lower respiratory tract specimens from patients admitted to the intensive care department and the drug resistance is relatively severe. The predominant strains with certain polymorphisms are mainly composed of the KPC-2-producing ST11-K64 and ST11-KL47 hv-CRKP isolates in the hospital.

The Emergence of Antimicrobial Resistance and Virulence Characteristics in Enterococcus Species Isolated from Bovine Milk.

Enterococcus spp., including E. faecalis and E. faecium, pose risks to dairy farms as opportunistic pathogens. The study evaluates antimicrobial resistance (AMR) and virulence characteristics of Enterococcus spp. isolated from bovine milk. Bile esculin agar was used to assess 1471 milk samples, followed by colony identification, gram staining, catalase tests, and 45 °C incubation. PCR analysis targeted E. faecalis and E. faecium in characteristic Enterococcus spp. colonies, with MALDI-TOF used for negative samples. Multiple tests, including disk diffusion, chromogenic VRE agar for vancomycin resistance, Vancomycin Etest® for MIC determination, and PCR for virulence factors (cylA, esp, efaA, ace, asa1, gelE, and hyl genes), were performed. Out of 100 identified strains, E. durans (30.66%), E. faecium (26.28%), and E. faecalis (18.25%) were predominant. AMR in Enterococcus spp. varied, with the highest rates against rifampicin (27%), tetracycline (20%), and erythromycin (18%). Linezolid (5%), vancomycin, ciprofloxacin, and teicoplanin (3% each) had lower prevalence. E. faecium and E. faecalis showed high AMR to rifampicin, erythromycin, and tetracycline. Thirty-two strains (18.98%) grew on VRE Chromoselect agar, while 4 (2 E. faecalis and 2 E. faecium) showed vancomycin resistance by MIC values. E. faecalis carried gelE (45.5%) and asa1 (36%), and E. gallinarum had 9.1% with the asa1 gene. Detecting resistant Enterococcus in bovine milk supports control strategies for enterococci on dairy farms, highlighting AMR concerns in the food chain.

Genomic Features of Antimicrobial Resistance in Staphylococcus pseudintermedius Isolated from Dogs with Pyoderma in Argentina and the United States: A Comparative Study.

Staphylococcus pseudintermedius is the most common opportunistic pathogen in dogs and methicillin resistance (MRSP) has been identified as an emerging problem in canine pyoderma. Here, we evaluated the antimicrobial resistance (AMR) features and phylogeny of S. pseudintermedius isolated from canine pyoderma cases in Argentina (n = 29) and the United States (n = 29). 62% of isolates showed multi-drug resistance. The AMR genes found: mecA, blaZ, ermB, dfrG, catA, tetM, aac(6')-aph(2″), in addition to tetK and lnuA (only found in U.S. isolates). Two point mutations were detected: grlA(S80I)-gyrA(S84L), and grlA(D84N)-gyrA(S84L) in one U.S. isolate. A mutation in rpoB (H481N) was found in two isolates from Argentina. SCCmec type III, SCCmec type V, ΨSCCmec57395 were identified in the Argentinian isolates; and SCCmec type III, SCCmec type IVg, SCCmec type V, and SCCmec type VII variant in the U.S. cohort. Sequence type (ST) ST71 belonging to a dominant clone was found in isolates from both countries, and ST45 only in Argentinian isolates. This is the first study to comparatively analyze the population structure of canine pyoderma-associated S. pseudintermedius isolates in Argentina and in the U.S. It is important to maintain surveillance on S. pseudintermedius populations to monitor AMR and gain further understanding of its evolution and dissemination.

Analysis of multidrug-resistant determinants of clinically isolated Acinetobacter baumannii CYZ via whole genome sequencing.

Acinetobacter baumannii is a multidrug-resistant coccobacillus responsible for severe nosocomial infectious diseases. This study mainly focuses on investigating the antimicrobial resistance features of a clinically isolated strain (A. baumannii CYZ) using the PacBio Sequel II sequencing platform. The chromosomal size of A. baumannii CYZ is 3,960,760 bp, which contains a total of 3803 genes with a G + C content of 39.06%. Functional analysis performed using the Clusters of Orthologous Groups of Proteins (COGs), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, as well as the Comprehensive Antibiotic Resistance Database (CARD) revealed a complicated set of antimicrobial resistance determinants in the genome of A. baumannii CYZ, which were mainly classified into multidrug efflux pumps and transport systems, β-lactamase relative and penicillin-binding proteins, aminoglycoside modification enzymes, alternation of antibiotic target sites, lipopolysaccharide relative, and other mechanisms. A total of 35 antibiotics were tested for the antimicrobial susceptibility of A. baumannii CYZ, and the organism exhibited a stronger antimicrobial resistance ability. The phylogenetic relationship indicated that A. baumannii CYZ has high homology with A. baumannii ATCC 17978; however, the former also exhibited its specific genome characteristics. Our research results give insight into the genetic antimicrobial-resistant features of A. baumannii CYZ as well as provide a genetic basis for the further study of the phenotype.

Genomic characterization of carbapenem-resistant Klebsiella oxytoca complex in China: a multi-center study.

Carbapenem-resistant (CR) Klebsiella oxytoca complex can be associated with high mortality, emerging as a new threat to the public health. K. oxytoca complex is phylogenetically close to K. pneumoniae, one of most common species associated with multidrug resistance in Enterobacterale. The latest research showed that K. oxytoca is a complex of six species. Currently, the epidemiological and genomic characteristics of CR K. oxytoca complex in China are still unclear. Here, we conducted a multi-center study on 25 CR K. oxytoca complex collected from five representative regions in China. These isolates were, respectively, recovered from respiratory tract (12 cases, 48.0%), abdominal cavity (5 cases, 20.0%), blood (4 cases, 16.0%), urine tract (3 cases, 12.0%) and skin or soft tissue (1 cases, 4.0%). Among them, 32.0% (8/25) of patients infected with K. oxytoca complex had a poor prognosis. In this study, three K. oxytoca complex species were detected, namely K. michiganensis, K. oxytoca and K. pasteurii, among which K. michiganensis was the most common. Three carbapenemase genes were identified, including blaNDM-1 (10, 38.5%), blaKPC-2 (9, 34.6%) and blaIMP (6 blaIMP-4 and 1 blaIMP-8; 7, 26.9%). Subsequent multilocus sequence typing identified various sequence types (STs), among which ST43, ST92 and ST145 were relatively common. Different from the clonal dissemination of high-risk carbapenem-resistant K. pneumoniae strains, our research revealed a polyclonal dissemination characteristic of CR K. oxytoca complex in China. S1-nuclease PFGE and Southern blot experiment showed that carbapenemase genes were encoded in plasmids of different sizes. Two blaNDM-harboring plasmids were subsequently sequenced, and were characterized to be IncX3 and IncC incompatibility groups, respectively. This is the first multi-center study of CR K. oxytoca complex in China, which improved our understanding of the prevalence and antimicrobial resistance characteristics of CR K. oxytoca complex in China.

Identification and characterisation of antimicrobial resistance of Enterococcus spp. isolated from pork and poultry meat

SummaryThere is a great concern on the presence of antimicrobial‐resistant bacteria in meat, since they can cause adverse effects in the consumers' health. The purpose of this work was to identify and characterise the antimicrobial resistance of Enterococcus spp. isolated from meat. A total of 209 meat samples (forty pork, fifty chicken, fifty‐one turkey, thirty‐one duck, and thirty‐seven quail) were collected at retail level. E. faecalis was the dominant enterococci isolated from all the types of meat evaluated, followed by E. faecium, E. gallinarum, and E. hirae, among others which were also isolated. Of the 317 strains evaluated for antimicrobial resistance 48 (15.14%) were multi‐resistant. Most of the multi‐resistant strains were E. faecium and E. faecalis, and in lesser extent E. gallinarum and E. hirae. Multi‐resistant strains were isolated from all the types of meat studied, mainly from turkey (sixteen strains), chicken (fifteen strains), and quail (fourteen strains). Two multi‐resistant strains showed resistance to vancomycin (E. faecium isolated from turkey meat, and E. faecalis isolated from quail meat). Resistance to tigecycline, teicoplanin, linezolid and quinolones was found among enterococci isolates. Special measures should be taken to avoid faecal contamination of carcasses in order to reduce enterococci prevalence in meat.

Genomic characterisation of a blaKPC-2- and mcr-10-co-harbouring Enterobacter kobei isolate with high-level resistance to colistin and carbapenems

The emergence and spread of colistin resistance in carbapenem-resistant Enterobacteriaceae pose a serious threat to human and animal health. This work aimed to characterize the genetic features of antimicrobial resistance of a carbapenem and colistin resistant Enterobacter kobei SCLZS19 from hospital sewage by using whole genome sequencing. Antimicrobial susceptibility tests were performed by using the disk diffusion method. Whole genome sequencing of SCLZS19 was carried out on the HiSeq 2000 combined with PacBio RSII platforms. Sequence type, plasmid incompatibility types, resistance genes, and insertion elements were identified using the MLST, PlasmidFinder, ResFinder, and ISfinder, respectively. Conjugation assays were performed using both broth- and filter-based methods with the azide-resistant Escherichia coli J53 as the recipient. The function of the mcr-9-like variant was determined by gene cloning. E. kobei SCLZS19 has a 4,862,177-bp circular chromosome, and nine circular plasmids ranging in size from 4,120 bp to 282,472 bp. It carries 11 antibiotic resistance genes (ARGs), and 10 of them are located on plasmids. The colistin resistance gene mcr-10 is located on a 118,766-bp non-transferable IncF (Y3:A-:B-) plasmid. The carbapenemase gene blaKPC-2 is carried by a self-transmissible IncP6 plasmid which is epidemic in China. In addition, SCLZS19 also carries a mcr-9-like variant on a IncHI2 (ST1) plasmid. Cloning assay shows that the mcr-9-like variant does not mediate colistin resistance in E. coli DH5α. The findings highlight that carbapenem- and colistin-resistant Enterobacterales from water environment may serve as a reservoir for clinically significant ARGs, and continuous surveillance is required.

Emergence of chromosomally located blaCTX-M-14b and qnrS1 in Salmonella enterica serotype Kentucky ST198 in China

Highly fluoroquinolone-resistant Salmonella enterica serotype Kentucky has become widespread in recent years, largely associated with the spread of sequence type 198 (ST198), which often leads to multidrug resistance. Research on the genomic epidemiology of Salmonella Kentucky in China is currently uncommon. In this study, we analysed the genomic epidemiology and antimicrobial resistance characteristics of Salmonella Kentucky ST198 collected from foodborne disease surveillance in Shenzhen, China, during 2010-2021, using whole-genome sequencing and antibiotic susceptibility testing. In addition, 158 global Salmonella Kentucky ST198 genomes were included for comparison. Among 8559 Salmonella isolates, 43 Salmonella Kentucky ST198 isolates were detected during 2010-2021. The global Salmonella Kentucky ST198 evolutionary tree was divided into five clades, with Shenzhen isolates distributed in clades 198.1, 198.2-1 and 198.2-2, mainly clustered with Chinese strains. Strains in clade 198.2 dominated in Shenzhen and all of them showed multidrug resistance. Nine strains showed high resistance to ceftriaxone, which was associated with blaCTX-M-14b in clade 198.2-1, which was demonstrated to be located on the chromosome. Fifteen strains showed high resistance to ciprofloxacin, which was associated with carriage of qnrS1 in clade 198.2-2. qnrS1 was first located on an IncHI2 plasmid and then transferred into the chromosome. Here we report the genomic and antimicrobial resistance characterisation of Salmonella Kentucky ST198 in Shenzhen. Of particular concern, we identified for the first time a clade 198.2-1 isolate carrying blaCTX-M-14b as well as chromosomally located qnrS1 in clade 198.2-2 of Salmonella Kentucky ST198 in China, highlighting the necessity of surveillance of clade 198.2.

Prevalence and genetic diversity of multidrug-resistant Salmonella Typhimurium monophasic variant in a swine farm from China.

Salmonella 4,[5],12:i:-, a monophasic variant of S. Typhimurium, has become a global serovar causing animal and human infections since its first emergence in the late 1980's. Several previous studies showed the increasing prevalence of S. 4,[5],12:i:- in China, most of which were from swine with multidrug resistance (MDR) profiles. However, the molecular characteristic and evolution of S. 4,[5],12:i:- in the same swine farm are still unknown. In this study, a total of 54 S. enterica strains were isolated from different fattening pigs aged 1, 3, and 6 months, most of which belonged to S. 4,[5],12:i:-. Whole-genome sequencing revealed that all 45 S. 4,[5],12:i:- strains belonged to ST34 and were further divided into two different ribosomal STs and nine different core-genome STs. Phylogenetic analysis of 286 S. 4,[5],12:i:- strains in China, including 241 from the EnteroBase Salmonella database, revealed the genetic diversity of S. 4,[5],12:i:- and indicated that S. 4,[5],12:i:- in this swine farm might have multiple origins. Three different IncHI2 plasmids carrying various resistance genes were characterized by nanopore sequencing and could be conjugated to Escherichia coli. The colistin resistance gene mcr-1 and ESBLs gene blaCTX - M-14 were co-located on the chromosome of one strain. The dynamic changes in antimicrobial resistance regions and transferability of IncHI2 plasmids, as well as the chromosomal location of resistance genes, facilitated the diversity of the antimicrobial resistance characteristics in S. 4,[5],12:i:-. Since the swine farm is regarded as the important reservoir of MDR S. 4,[5],12:i:-, the prevalence and evolution of S. 4,[5],12:i:- from swine farms to pig products and humans should be continually monitored.

Molecular Surveillance of MRSA in Raw Milk Provides Insight into MRSA Cross Species Evolution.

Methicillin-resistant Staphylococcus aureus (MRSA) in foods has been associated with severe infections in humans and animals worldwide. In the present study, the molecular characteristics of livestock-associated MRSA (LA-MRSA) and human-associated MRSA (hMRSA) isolates obtained in China, as well as MRSA isolates obtained from raw milk in 2018, were investigated. In total, 343 (20.38%; 343/1,683) S. aureus isolates were obtained from 1,683 raw milk samples from 100 dairy farms in 11 provinces across China. Among these, 49 (2.91%; 49/1,683) were mecA-positive MRSA. All LA-MRSA isolates were resistant to penicillin and highly resistant to erythromycin, sulfisoxazole, and clindamycin. Bioinformatic analysis the 49 genomes of LA-MRSA and 71 previously published hMRSA genomes isolated from Chinese individuals in 2018 indicated that blaZ, erm, ant(6)-Ia, aph(3')-III, tet(K), cat, and aph(2″)-Ia were more prevalent in MRSA from raw milk (P < 0.05) compared to hMRSA. Additionally, hMRSA isolates were more significantly associated with ST5 (P < 0.01) compared to LA-MRSA; in contrast, ST338 was more prevalent among LA-MRSA isolates (P < 0.01). Likewise, the SCCmec type II was only detected in hMRSA isolates, whereas SCCmec type V and IV were more prevalent among LA-MRSA (P < 0.01). Furthermore, core-genome phylogenetic analysis showed the endemic characteristics of LA-MRSA in local provinces, as well as the close evolutionary relationships between MRSA from cattle and humans. Finally, homology analysis of mecA and blaZ genetic contexts revealed a high possibility of horizontal transmission of MRSA resistance genes among raw milk-associated and hMRSA strains, which increases the risk for public health. IMPORTANCE Methicillin-resistant Staphylococcus aureus (MRSA) is considered a public health concern as it is resistant to multiple antibiotics, thus being in zoonotic transmission of antibiotic resistance genes. MRSA causes serious public health issues and leads to hard-to-treat infections in humans and animals; therefore, it was meaningful to determine the prevalence of MRSA in raw milk samples and investigate phenotype and genotype of antimicrobial resistance and molecular characteristics in livestock-associated MRSA (LA-MRSA) and human-associated MRSA (hMRSA) in China, which could provide a theoretical basis for preventing and controlling the spread of MRSA between livestock and humans.