Explore the vast range of titles available.

Multilocus sequence typing (MLST) indexes the sequence variation present in a small number (usually seven) of housekeeping gene fragments located around the bacterial genome. Unique alleles at these loci are assigned arbitrary integer identifiers, which effectively summarizes the variation present in several thousand base pairs of genome sequence information as a series of numbers. Comparing bacterial isolates using allele-based methods efficiently corrects for the effects of lateral gene transfer present in many bacterial populations and is computationally efficient. This 'gene-by-gene' approach can be applied to larger collections of loci, such as the ribosomal protein genes used in ribosomal MLST (rMLST), up to and including the complete set of coding sequences present in a genome, whole-genome MLST (wgMLST), providing scalable, efficient and readily interpreted genome analysis.

Xiaorong Wang; Jianchu Zhang, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Number 1277, Jie Fang Rode, Wuhan, Hubei, 430022, People’s Republic of China, Tel + 86-27-85726707, Email rong-100@163.com; zsn0928@163.comPurpose: To investigate the molecular epidemiology and risk factors of carbapenem-resistant Klebsiella pneumoniae (CRKP) infection.Patients and Methods: Patient’s clinical data and CRKP strains were collected from November 2017 to December 2018 at a tertiary hospital in Wuhan, China. The antimicrobial susceptibilities, carbapenem-resistant genes, multi-locus sequence typing (MLST), homologous analysis, and risk factors for CRKP were determined.Results: A total of 203 CRKP strains were isolated, and 98.5% (200/203) of patients were nosocomially infected. The mortality rate was 17.7% (36/203). All 203 strains were confirmed as carbapenemases -producing strains. The most predominant carbapenemase gene was blaIMP-4 (81.3%, 165/203), followed by blaKPC-2 (25.1%, 51/203) and blaNDM-1 (23.2%, 47/205). Of the 203 strains, 28 (13.8%) had both blaKPC-2 and blaIMP-4 genes, 23 (11.3%) had both blaIMP-4 and blaNDM-1 genes, 20 (9.9%) had blaKPC-2, blaIMP-4 and blaNDM-1 three genes. MLST analysis showed that there were 48 ST typologies (including 7 new STs), of which ST-11 was the most prevalent (59.6%, 121/203). Phylogenetic analysis showed that 203 CRKP isolates came from 7 clusters and exhibited a strong correlation with the isolation source. eBURST analyses indicated that CRKP isolates have undergone different evolutionary processes. Patients with ST-11 CRKP underwent more mechanical ventilation (50% vs 32.9%, P=0.020) and gastric catheterization (15.7% vs 6.1%, P=0.042) within 3 months before sample collection, and also had higher drug-resistance rate than non-ST-11 CRKP. Comparing with CSKP (carbapenem-sensitive Klebsiella pneumoniae), gastrointestinal disease (odds ratio [OR]=6.168, P=0.003), nosocomial infection (OR=5.573, P=0.012), antibiotic exposure (OR=4.131, P=0.004), urinary catheterization (OR=3.960, P=0.031) and venous/arterial catheterization (OR=2.738, P=0.026) within the preceding 3 months were independent risk factors for CRKP infection.Conclusion: The IMP-4 was the most predominant carbapenemase and blaIMP-4 bearing Klebsiella pneumoniae ST-11 was spreading in the hospital. Nosocomial infections, antibiotic exposure, and urinary and venous/arterial catheterization within 3 months were the risk factors for developing CRKP infection.

Enterococcus faecium is emerging as an important cause of multidrug resistance and hospital acquired infections, special attention being paid to the vancomycin resistant species. Therefore, the characterization of pathogenic strains/isolates plays an important role in the epidemiology of infectious diseases. The enterococcal rate was determined from wastewaters in Cluj-Napoca area. As presence of E. faecium was detected, a number of isolates from wastewater, birds and humans were epidemiologically analyzed according to the MLST website. Comparisons were performed against a collection of available isolates, with multiple origins, contained in the MLST database. Out of the Enterococcus isolates collected from wastewater, 11 were identified as E. faecalis (40.74%); 8 as E. casseliflavus (29.62%); 5 as E. faecium (18.50%); 2 as E. gallinarum (7.40%) and one isolate as E. durans. Based on the MLST data and using the eBURST algorithm, the isolates of E. faecium sampled from Romania were split in three groups: one group comprised isolates from human hosts and wastewater (Cj316, 106/6, Cj197, Cj22, 129/6, Cj117, Cj24, 284/7, and 43/7), while the second (G9, G10-2, G7, G3-2, and G9-1) and the third group (G8, G6, and 40/7) originated from bird hosts. The rest of the isolates were not joined in a particular group, assuming the lack of a phylogenetic bond between these isolates. The obtained data suggested the existence of at least two phylogenetic lines of E. faecium in Romania: a line that had mainly human host prevalence, while in the other line the animal hosts dominated. 

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a threat to public health, most notably as a superbug causing nosocomial infections. Patients in the intensive care unit (ICU) are at increased risk of hospital-acquired K pneumoniae infection, especially CRKP. This study was conducted to investigate the frequency of gastrointestinal and nasopharyngeal K pneumoniae colonization and its contribution to infections in ICU patients. A 3-month prospective cohort study was performed in which 243 ICU patients were screened for intestinal and nasopharyngeal carriage of K pneumoniae at admission and once per week thereafter. The colonization and clinical infection isolates were analyzed by antimicrobial susceptibility testing to identify CRKP and were characterized by multilocus sequence typing (MLST) and whole-genome sequencing combined with epidemiological data to investigate the resistance mechanisms and assess the possible transmitted infection. Twenty-eight percent (68 of 243) of patients tested positive for carriage of K pneumoniae immediately upon admission to ICU, 54% (37 of 68) of which were nonduplicate CRKP isolates. Patients with carbapenem-susceptible K pneumoniae (CSKP) colonization at admission were more likely to acquire CRKP colonization during the ICU stay compared with patients without K pneumoniae colonization at admission. The incidence of subsequent CRKP infection in the baseline CSKP (32.3%, 10 of 31) and CRKP (45.9%, 17 of 37) carrier group was significantly higher than that of the baseline non-KP carrier group (8.6%, 15 of 175). The risk factors associated with acquired CRKP colonization during the ICU stay among negative CRKP colonization at admission included previous exposure to carbapenem, tigecycline or β-lactam/β-lactamases inhibitor, and invasive processes or surgical operations. Sixty-four percent (27 of 42) of patients with K pneumoniae infection were colonized by clonally related K pneumoniae strains according to enterobacterial repetitive intergenic consensus sequence-polymerase chain reaction analysis. ST11 (72%, 53 of 74) was the most predominant MLST type of clonally related CRKP isolate colonizing these patients, followed by ST15 (26%, 19 of 74). The colonization of K pneumoniae may increase the incidence of corresponding K pneumoniae infection in critically ill patients in the ICU. High prevalence of ST11 CRKP (due to blaKPC-2) carriage and infection in ICU was observed.

We have developed a new multilocus typing (MLST) scheme useful for all Treponema pallidum lineages after the analysis of 121 complete genome sequences of this species. The new scheme can be used directly with uncultured clinical samples, thus providing an excellent contribution to the molecular surveillance of syphilis and other treponematoses. The application of this MLST scheme to over 500 samples from all lineages and main geographical regions has revealed similar levels of genetic variation within them. Furthermore, the analyses show a complex pattern of spread, with global and local contributions to the observed distribution of genetic variation in the syphilis-producing sublineages. The new scheme represents a significant improvement over previous proposals and also reveals unsuspected levels of variability in T. pallidum lineages.

Qian Li,1 Qinghua Qiu,1 Hanfu Gu,1 Zhaoye Huang,2 Yujia Luo,2 Xuemin Guo1,3,4 1Clinical Laboratory Center, Meizhou People’s Hospital, Meizhou, Guangdong, People’s Republic of China; 2Medical College of Jiaying University, Meizhou, Guangdong, People’s Republic of China; 3Guangdong Engineering Technological Research Center of Clinical Molecular Diagnosis and Antibody Drugs, Meizhou, Guangdong, People’s Republic of China; 4Guangdong Provincial Clinical Research Center for Laboratory Medicine, Guangzhou, Guangdong, People’s Republic of ChinaCorrespondence: Xuemin Guo, Email guoxuemin@mzrmyy.comBackground: Rising Neisseria gonorrhoeae cephalosporin resistance worldwide is compromising first-line therapy, yet data from underrepresented regions of China are lacking. This study provided a comprehensive analysis of antimicrobial susceptibility and the molecular epidemiology of cephalosporin-resistant strains from Meizhou.Methods: Neisseria gonorrhoeae isolates were collected from Meizhou People’s Hospital between September 2020 and December 2024. The minimum inhibitory concentrations (MICs) were determined by the broth microdilution method. Isolates with ceftriaxone or cefixime MIC > 0.125 mg/L were genotyped by Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST), multilocus sequence typing (MLST), and Neisseria gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR).Results: A total of 195 Neisseria gonorrhoeae isolates were collected. Among them, 48 (24.6%) showed cephalosporin resistance (ceftriaxone or cefixime MIC > 0.125 mg/L). Over the study period, ceftriaxone resistance rose from 0% (0/14) in 2020 to 24.1% (7/29) in 2024, while cefixime resistance declined from 28.9% (4/14) in 2020 to 6.3% (2/32) in 2023 and then rebounded to 24.1% (7/29) in 2024. Genotypic analysis of the 48 cephalosporin-resistant isolates identified three predominant penA types: XXXIV, LX, and XIII. Typing by MLST, NG‑MAST, and NG‑STAR revealed a diverse population with multiple sequence types. Initially, penA-XXXIV and penA-XIII were predominant. However, since 2022, penA-LX (NG-STAR penA-60.001) strains underwent significant clonal expansion and became the dominant resistant lineage. Using goeBURST, MLST ST7363 was placed at the center of the minimum spanning tree, with ST1903 and ST1901 as single- and double-locus variants, respectively. Subsequent NG-MAST phylogeny confirmed penA-specific clustering, indicating the emergence of distinct genotypic groups associated with these allelic changes.Conclusion: This study reveals a clonal succession in Meizhou, where penA-60.001 strains became more prevalent than pre-existing cephalosporin-resistant lineages. This shift highlights the persistent threat of evolving resistance in Neisseria gonorrhoeae and emphasizes the need for sustained genomic surveillance to guide targeted interventions.Keywords: Neisseria gonorrhoeae, cephalosporin-resistant, NG-STAR, MLST, NG-MAST

Acinetobacter baumannii is especially known as a cause of nosocomial infections worldwide. It shows intrinsic and acquired resistances to numerous antimicrobial agents, which can render the treatment difficult. In contrast to the situation in human medicine, there are only few studies focusing on A. baumannii among livestock. In this study, we have examined 643 samples from turkeys reared for meat production, including 250 environmental and 393 diagnostic samples, for the presence of A. baumannii. In total, 99 isolates were identified, confirmed to species level via MALDI-TOF-MS and characterised with pulsed-field gel electrophoresis. Antimicrobial and biocide susceptibility was tested by broth microdilution methods. Based on the results, 26 representative isolates were selected and subjected to whole-genome sequencing (WGS). In general, A. baumannii was detected at a very low prevalence, except for a high prevalence of 79.7% in chick-box-papers (n = 118) of one-day-old turkey chicks. The distributions of the minimal inhibitory concentration values were unimodal for the four biocides and for most of the antimicrobial agents tested. WGS revealed 16 Pasteur and 18 Oxford sequence types, including new ones. Core genome MLST highlighted the diversity of most isolates. In conclusion, the isolates detected were highly diverse and still susceptible to many antimicrobial agents.

The paper presents various issues related to the increasing drug resistance of Neisseria gonorrhoeae and the occurrence and spread of multidrug-resistant clones. One of the most important is the incidence and evolution of resistance mechanisms of N. gonorrhoeae to beta-lactam antibiotics. Chromosomal resistance to penicillins and oxyimino-cephalosporins and plasmid resistance to penicillins are discussed. Chromosomal resistance is associated with the presence of mutations in the PBP2 protein, containing mosaic variants and nonmosaic amino acid substitutions in the transpeptidase domain, and their correlation with mutations in the mtrR gene and its promoter regions (the MtrCDE membrane pump repressor) and in several other genes, which together determine reduced sensitivity or resistance to ceftriaxone and cefixime. Plasmid resistance to penicillins results from the production of beta-lactamases. There are different types of beta-lactamases as well as penicillinase plasmids. In addition to resistance to beta-lactam antibiotics, the paper covers the mechanisms and occurrence of resistance to macrolides (azithromycin), fluoroquinolones and some other antibiotics. Moreover, the most important epidemiological types of multidrug-resistant N. gonorrhoeae, prevalent in specific years and regions, are discussed. Epidemiological types are defined as sequence types, clonal complexes and genogroups obtained by various typing systems such as NG-STAR, NG-MAST and MLST. New perspectives on the treatment of N. gonorrhoeae infections are also presented, including new drugs active against multidrug-resistant strains.

One of the most important aquatic parasites in industrialized countries, Cryptosporidium spp., is a major cause of diarrheal disease in humans and animals worldwide. The contingent evolution of cryptosporidia with hosts, host adaptation, and geographic variation contributed to the creation of species subtypes, thereby shaping their population genetic structures. Multilocus typing tools for population genetic characterizations of transmission dynamics and delineation of mechanisms for the emergence of virulent subtypes have played an important role in improving our understanding of the transmission of this parasite. However, to better understand the significance of different subtypes with clinical disease manifestations and transmission risks, a large number of samples and preferably from different geographical areas need to be analyzed. This review provides an analysis of genetic variation through multilocus sequence typing, provides an overview of subtypes, typing gene markers for Cryptosporidium parvum, Cryptosporidium hominis, Cryptosporidium muris and Cryptosporidium andersoni genotypes and an overview of the hosts of these parasites.