Multiple-locus Variable-number Tandem Repeat Research Articles

A single-center analysis of clonal transmission of carbapenem-resistant Acinetobacter baumannii among intensive care unit patients during the COVID-19 pandemic

Carbapenem-Resistant Acinetobacter baumannii (CRAB) outbreak in intensive care units (ICUs) is a significant problem for healthcare facilities. In this study, we aimed to investigate the occurrence of CRAB isolates among ICU-admitted patients during the three waves of the COVID-19 pandemic in Iran using Multiple-Locus Variable Number Tandem-Repeat Analysis (MLVA). We obtained 50 (A) baumannii isolates from tracheal aspirate and blood culture samples. In the disc diffusion method, all isolates were cefotaxime, ceftriaxone, and cefepime-resistant, while 98% (49/50) of isolates were resistant to piperacillin, piperacillin-tazobactam, ceftazidime, and ciprofloxacin. Levofloxacin and tobramycin resistance was found in 76% (38/50) of isolates. In the microbroth dilution test all isolates were resistant to imipenem, 98% (49/50) to meropenem, 68% (34/50) to colistin, and 20% (10/50) to polymyxin (B) Based on the PCR findings, all isolates harbored blaOXA−40, ISAba-1, and int-2 genes. There were no isolates found that have the blaOXA−58, blaOXA−143, blaVEB−1, blaVIM, and int-3 genes. Among Extended-spectrum beta-lactamases (ESBL) genes, blaCTX−M, blaTEM, blaSHV, blaGES, and blaPER−1 have a prevalence of 42% (21/50), 84% (42/50), 58% (29/50), 78% (39/50), and 54% (27/50), respectively. 74% (37/50) of the isolates had the blaOXA−23 gene, while all of the isolates carried the blaOXA−40 gene. Among MBL genes, blaIPM, blaGIM, blaSIM, and blaNDM−1 have a prevalence of 20% (10/50), 8% (4/50), 22% (11/50), and 60% (30/50), respectively. The prevalence of int-1 was documented as 74% (37/50). Accordingly, all isolates were identified as CRAB. The co-existence of blaOXA−23/int-2 and blaOXA−23/isaba-1 was 74% (37/50). The co-existence of blaNDM−1/ISAba-1 was observed in 30 (60%) isolates. Using an 80% similarity threshold on the dendrogram constructed through MLVA typing, all isolates were grouped into two clusters: cluster A with 9 isolates from wave 3, and cluster B with 41 isolates from waves 3, 4, and 5. Our study confirms a clonal transmission of CRAB during the study period and suggests using molecular typing methods like MLVA in healthcare settings to identify dominant clones, antibiotic resistance patterns, and transmission routes. This will help to better manage the emergence and spread of antibiotic-resistant strains in future outbreaks.

Molecular epidemiology of brucellosis in Asia: insights from genotyping analyses.

Brucellosis infects humans and animals worldwide but is particularly prevalent in Asia. In many Asian countries, molecular diagnostic tools for accurate molecular diagnostics and molecular epidemiology are lacking. Nonetheless, some countries have conducted in-depth molecular epidemiological studies. The objective of this study was to reveal the genetic relationships, geographic origins, and distributions of Brucella strains across Asia for two primary species, B. abortus and B. melitensis. For this, we systematically searched genotyping data from published studies on the molecular epidemiology of Brucella species for both humans and livestock in Asia. We used data from multilocus sequence typing (MLST), multiple-locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing analysis of Brucella strains. We also analyzed the MLVA genotypes of 129 B. abortus isolates and 242 B. melitensis isolates with known origins in Asia from an online MLVA database using MLVA-11 data in minimum spanning trees and MLVA-16 data in neighbor-joining trees. We found that the B. melitensis East Mediterranean lineage is predominant across the continent, with only a small number of samples from the Africa and Americas lineages, and none from the West Mediterranean lineage. The "abortus C" genotype was the most common group of B. abortus in Asia, with limited genetic variation for this species. Several studies also reported that Near Eastern countries frequently encounter human brucellosis cases of B. abortus from genotypes 42 and 43. Our study highlights the inconsistent collection of genetic data for Brucella species across Asia and a need for more extensive sampling in most countries. Finally, a consistent nomenclature is necessary to define various groupings of strains within a lineage (i.e., clade) so uniform terminology should denote particular genetic groups that are understood by all researchers.

Multiple-Locus Variable-Number Tandem Repeat Analysis of Helicobacter Pylori Strains Isolated from Biopsy Samples

Background: Multiple-locus variable-number tandem-repeat analysis (MLVA) is a reliable, fast, and useful method for conducting phylogenetic and genotyping analyses. However, its application in Helicobacter pylori typing is limited. Objectives: This study aimed to determine the genetic diversity of H. pylori strains isolated from biopsy samples using six variable loci in MLVA typing. Methods: Over one year, we collected 70 non-duplicative biopsy samples from patients at Rohani Hospital, Babol, in northern Iran. After DNA extraction, H. pylori strains were confirmed through the amplification of the glmM gene in the PCR test. Multiple-locus variable-number tandem-repeat analysis typing utilized six VNTR markers: VNTR-180, VNTR-263, VNTR-614, VNTR-607, VNTR-2181, and VNTR-2457. The PHYLOViZE software was employed to construct the phylogenetic tree. Results: Out of the 70 specimens, 43 tested positive for H. pylori. The phylogenetic tree revealed some strains with completely similar MLVA patterns. Our findings indicated that type 2 is the dominant type in this region, with most patients infected with this type exhibiting gastritis. Conclusions: The high allelic variability observed at VNTR-614, -607, and -2457 indicates high intraspecific variability for these markers in all isolates from our region. Consequently, these VNTRs can be considered ideal sites for typing.

High hemolytic activity of the Staphylococcus aureus spa t1081 among clonal complex 45 in Taiwan

BackgroundMethicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST) 45 was first reported in Taiwan in 2006. Since then, the prevalence of ST45 MRSA in clinical isolates has increased. This study was carried out to understand the changes in the proportions, evolutionary relationships, and infection advantages of ST45 and its related clones. Materials and methods: S. aureus including MRSA and MSSA (methicillin-sensitive S. aureus), and clonal complex (CC) 45 blood isolates were collected in 2000, 2005, and from January 2010 to August 2014. Molecular typing, multiple-locus variable-number tandem repeat analysis (MLVA) and single nucleotide polymorphism (SNP)-based phylogenetic analysis were performed. Fitness and virulence analyses were used to understand the infection advantages of the isolates. ResultsAmong the 67 CC45 isolates, only MSSA ST508 isolates were found in 2000 and 2005. Since 2010, the prevalence of MRSA has increased, t1081/ST45 has become dominant, and MRSA ST508 has been found. Phylogenetic analysis indicated that most of the ST45 isolates were located in a cluster distinct from those of ST508 and ST929. However, the t026 isolates clustered with the ST508 isolates rather than with the other ST45 isolates. Moreover, fitness and virulence analyses revealed that the t1081 isolates had higher hemolytic activity than the t026 and ST508 isolates did. ConclusionOur findings indicated that the increased prevalence of ST45 MRSA isolates from blood cultures in Taiwan was due to the t1081 isolates, and their high hemolytic activity may provide an infection advantage.

Bacillus anthracis in South Africa, 1975–2013: are some lineages vanishing?

The anthrax-causing bacterium Bacillus anthracis comprises the genetic clades A, B, and C. In the northernmost part (Pafuri) of Kruger National Park (KNP), South Africa, both the common A and rare B strains clades occur. The B clade strains were reported to be dominant in Pafuri before 1991, while A clade strains occurred towards the central parts of KNP. The prevalence of B clade strains is currently much lower as only A clade strains have been isolated from 1992 onwards in KNP. In this study 319 B. anthracis strains were characterized with 31-loci multiple-locus variable-number tandem repeat analysis (MLVA-31). B clade strains from soil (n = 9) and a Tragelaphus strepsiceros carcass (n = 1) were further characterised by whole genome sequencing and compared to publicly available genomes. The KNP strains clustered in the B clade before 1991 into two dominant genotypes. South African strains cluster into a dominant genotype A.Br.005/006 consisting of KNP as well as the other anthrax endemic region, Northern Cape Province (NCP), South Africa. A few A.Br.001/002 strains from both endemic areas were also identified. Subclade A.Br.101 belonging to the A.Br.Aust94 lineage was reported in the NCP. The B-clade strains seems to be vanishing, while outbreaks in South Africa are caused mainly by the A.Br.005/006 genotypes as well as a few minor clades such as A.Br.001/002 and A.Br.101 present in NCP. This work confirmed the existence of the rare and vanishing B-clade strains that group in B.Br.001 branch with KrugerB and A0991 KNP strains.

An Evaluation of the Lineage of Brucella Isolates in Turkey by a Whole-Genome Single-Nucleotide Polymorphism Analysis.

Brucellosis is a disease caused by the Brucella (B.) species. It is a zoonotic disease that affects farm animals and causes economic losses in many countries worldwide. Brucella has the ability to persist in the environment and infect the host at low doses. Thus, it is more important to trace brucellosis outbreaks, identify their sources of infection, and interrupt their transmission. Some countries already have initial data, but most of these data are based on a Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA), which is completely unsuitable for studying the Brucella genome. Since brucellosis is an endemic disease in Turkey, this study aimed to examine the genome of Turkish Brucella isolates collected between 2018 and 2020, except for one isolate, which was from 2012. A total of 28 strains of B. melitensis (n = 15) and B. abortus (n = 13) were analyzed using a core-genome single-nucleotide polymorphism (cgSNP) analysis. A potential connection between the Turkish isolates and entries from Sweden, Israel, Syria, Austria, and India for B. melitensis was detected. For B. abortus, there may be potential associations with entries from China. This explains the tight ties found between Brucella strains from neighboring countries and isolates from Turkey. Therefore, it is recommended that strict measures be taken and the possible effects of uncontrolled animal introduction are emphasized.

Molecular epidemiology and genomic features of Bordetella parapertussis in Shanghai, China, 2017-2022.

Pertussis is a highly contagious respiratory illness mainly caused by Bordetella pertussis (BP). Bordetella parapertussis (BPP) can induce symptoms compatible with pertussis, but has been underdiagnosed and underreported. The current pertussis vaccines offer low protection against BPP. Herein, we aim to reveal the epidemiology and genomic evolution of BPP in Shanghai, China. Children diagnosed with BPP infection from January 2017 to December 2022 in Shanghai, China were enrolled. We performed antimicrobial susceptibility testing (AST), multiple locus variable-number tandem repeat analysis (MLVA), and whole genome sequencing (WGS) analysis. A total of 260 international BPP genomes were chosen for comparison to investigate the genomic diversity and phylogenetic characteristics of Chinese strains within a global context. Sixty patients were diagnosed with BPP infection by culture, with the positive ratio of 3.5‰ (60/17337) for BPP in nasopharyngeal swap samples. The average age of patients was 4.5 ± 0.3 years. BPPs contained four MLVA types including MT6 (65.0%), MT4 (26.7%), untype-1 (6.7%) and MT5 (1.7%), and none of strains showed resistance to macrolides. All strains carried virulence genotype of ptxP37/ptxA13/ptxB3/ptxC3/ptxD3/ptxE3/fim2-2/fim3-10. MT4 and MT5 strains carried prn54, whereas MT6 and untype-1 BPPs expressed prn101. We identified two outbreaks after 2020 caused by MT4 and MT6 strains, each corresponding to distinct WGS-based phylogenetic lineages. The MT4-lineage is estimated to have originated around 1991 and has since spread globally, being introduced to China between 2005 and 2010. In contrast, the MT6-lineage was exclusively identified in China and is inferred to have originated around 2002. We revealed the genomic diversity of BPPs circulating in Shanghai, China, and reported the outbreaks of MT6 and MT4 BPPs after 2020. This is the first report on the emergence and regional outbreak of MT6 BPPs in the world, indicating that continuous surveillance on BPPs are thus required.

Virulent properties and genomic diversity of Vibrio vulnificus isolated from environment, human, diseased fish.

The incidence of Vibrio vulnificus infections, with high mortality rates in humans and aquatic animals, has escalated, highlighting a significant public health challenge. Currently, reliable markers to identify strains with high virulence potential are lacking, and the understanding of evolutionary drivers behind the emergence of pathogenic strains is limited. In this study, we analyzed the distribution of virulent genotypes and phenotypes to discern the infectious potential of V. vulnificus strains isolated from three distinct sources. Most isolates, traditionally classified as biotype 1, possessed the virulence-correlated gene-C type. Environmental isolates predominantly exhibited YJ-like alleles, while clinical and diseased fish isolates were significantly associated with the nanA gene and pathogenicity region XII. Hemolytic activity was primarily observed in the culture supernatants of clinical and diseased fish isolates. Genetic relationships, as determined by multiple-locus variable-number tandem repeat analysis, suggested that strains originating from the same source tended to cluster together. However, multilocus sequence typing revealed considerable genetic diversity across clusters and sources. A phylogenetic analysis using single nucleotide polymorphisms of diseased fish strains alongside publicly available genomes demonstrated a high degree of evolutionary relatedness within and across different isolation sources. Notably, our findings reveal no direct correlation between phylogenetic patterns, isolation sources, and virulence capabilities. This underscores the necessity for proactive risk management strategies to address pathogenic V. vulnificus strains emerging from environmental reservoirs.IMPORTANCEAs the global incidence of Vibrio vulnificus infections rises, impacting human health and marine aquacultures, understanding the pathogenicity of environmental strains remains critical yet underexplored. This study addresses this gap by evaluating the virulence potential and genetic relatedness of V. vulnificus strains, focusing on environmental origins. We conduct an extensive genotypic analysis and phenotypic assessment, including virulence testing in a wax moth model. Our findings aim to uncover genetic and evolutionary factors that drive pathogenic strain emergence in the environment. This research advances our ability to identify reliable virulence markers and understand the distribution of pathogenic strains, offering significant insights for public health and environmental risk management.

The Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) of Staphylococuss aureus clinical isolates recovered from the Provincial Specialist Hospital in Lublin, Poland

The Multiple-Locus Variable Number Tandem Repeat Analysis (MLVA) of <i>Staphylococuss aureus</i> clinical isolates recovered from the Provincial Specialist Hospital in Lublin, Poland

Multiple-Locus Variable-Number Tandem Repeat Analysis Genotyping of Biofilm-Producing Pseudomonas aeruginosa Clinical Isolates

Background: Pseudomonas aeruginosa (P. aeruginosa) significantly contributes to hospital-acquired infections. Objectives: This study aimed to investigate the genetic diversity of P. aeruginosa strains using multiple-locus variable-number tandem repeat analysis (MLVA) and to explore the relationship between biofilm production and antibiotic resistance. Methods: In this cross-sectional study, 79 P. aeruginosa isolates were collected. Antibiotic sensitivity was tested using the Kirby-Bauer method, and biofilm production capability was assessed through the microtiter plate method. Genetic diversity was evaluated by MLVA, analyzing eight variable-number tandem repeat (VNTR) loci: MS-213, MS-214, MS-207, MS-217, MS-222, MS-209, MS-77, and MS-172. Phylogenetic relationships were delineated using PHYLOViZ 2.0 software. Results: The patient cohort comprised 51.9% males, with the majority of samples (35.4%) obtained from urine. Ceftazidime (CAZ 30µg) showed the highest resistance rate at 77.2%. Notably, 92.4% of isolates were capable of forming biofilms, categorized as 22.7% weak, 28.7% moderate, and 46.5% strong. Phylogenetic analysis demonstrated variability across one or more VNTR loci. Simpson’s index (0.906) and Shannon-Weiner diversity indices (H: 3.466, J: 0.910, Hmax: 3.807, Hmin: 1.242) identified MS77 as the most informative marker for genetic diversity among the isolates. Conclusions: The study highlights an alarming trend in antibiotic resistance, underscoring the necessity of regular monitoring. The findings confirm that MLVA is a straightforward, rapid genotyping method suitable for assessing the genetic diversity of P. aeruginosa.

CRISPR 2 spacer architecture analysis and virulotyping for epidemiological study of Salmonella enterica subsp. Enterica circulating in northern Thailand (2015 -2017)

Background: Salmonella enterica subsp. enterica, particularly serotype S. 4[5],12:i:-, S. Typhimurium, and S. Enteritidis, represents a significant causative agent of diarrhea, particularly impacting children and immunocompromised individuals on a global scale. Molecular typing of Salmonella spp. has a vital role in understand Salmonella epidemiology. Objective: The objective of this study is to utilize CRISPR 2 spacer analysis coupled with multiple-locus variable number tandem-repeat (VNTR) analysis and virulotyping to perform molecular typing and potential subtyping of Salmonella spp. Materials and methods: CRISPR 2 - multiple-locus variable number tandem-repeat (VNTR) analysis, complemented by additional virulotyping, were performed to rapidly characterize those Salmonella isolates including eight unidentified strains. Serotype-specific CRISPR 2 amplicons were subjected to sequencing and the obtained sequences were blasted with corresponding whole-genome sequencing (WGS) data in order to extract CRISPR 2 information, especially the number and sequence of spacers which were then utilized to predict Salmonella serotypes. Moreover, the similar CRISPR 2 spacer architectures to the corresponding WGS offered the prediction of multilocus sequence types (MLST). Results: S. 4,[5],12:i:-, S. Typhimurium, S. Enteritidis, S. Weltevraden, and S. Derby exhibited distinct clustering, while eight unidentified Salmonella serotypes displayed unique CRISPR 2-MLVA profiles. Through subsequent sequence analysis and comparison with publicly available whole-genome sequencing data, serotype-specific CRISPR 2 amplicon lengths and spacer architectures were unveiled, enabling precise prediction of MLST types. Intriguingly, a linear correlation emerged between CRISPR 2 amplicon length (500-2000 bps) and the number of spacers (6-32) across diverse Salmonella serotypes. Critically, the molecular signatures of CRISPR 2 amplicons accurately predicted the identity of eight unknown Salmonella isolates, aligning with conventional serotyping standards. Furthermore, MLST sequences for prevalent S. 4,[5],12:i:-, S. Typhimurium, and S. Enteritidis were unveiled as ST 34, ST 19, and ST 10, respectively. Subtyping of S. 4,[5],12:i:- using the sopE1 procession (a bacteriophage gene) revealed two major subtypes within ST 34. These subtypes encompassed all six virulent genes, including InvA, bcfC, csgA, agfA, sodC1, and gipA, either with sopE1 (N=8) or without sopE1 (N=10). These findings contribute preliminary insights into the genetic diversity and subtyping of S. 4,[5],12:i:-. Conclusion: The combination of CRISPR 2 sequence analysis and virulotyping emerged as a potent epidemiological tool, facilitating the identification of Salmonella serotypes and potentially informative subtypes, thereby aiding in the surveillance, and tracking of Salmonella transmission in northern Thailand.

Occurrence, antimicrobial resistance, and molecular characteristics of Salmonella enterica serovar 1,4,[5],12:i:- from food and patients in China

Salmonella enterica serovar Typhimurium monophasic variant 1,4,[5],12:i:- is increasingly responsible for human infections worldwide. However, studies assessing the prevalence and epidemiological characteristics of this emerging serovar are lacking in China. Here, a collection of 125 S. Typhimurium-like strains derived from food and patients in China between 2011 and 2019 were analyzed to investigate the occurrence ratio of S. 1,4,[5],12:i:-. Among them, 23.2% (22/95) of food-related isolates and 70.0% (21/30) of human isolates were assigned as S. 1,4,[5],12:i:-. Only two strains were sequence type (ST) 19; the rest all belonged to ST34. These isolates were further divided into 29 multiple locus variable-number tandem repeat analysis (MLVA) profiles, with the same dominant profile present in both food-source and human isolates. More than 90.0% of S. 1,4,[5],12:i:- isolates were multidrug-resistant. The high prevalence of blaCTX-M (33.3%, 7/21) in extended-spectrum β-lactamase-producing S. 1,4,[5],12:i:- isolates from patients identified here will raise clinical concern over human salmonellosis treatment. Twelve different deletion types of the fljAB operon region associated with the loss of phase 2 flagellar antigen were identified. These results suggested that the Chinese S. 1,4,[5],12:i:- strains consist of multiple distinct clones and their high rates of prevalence and multidrug resistance could constitute potential risks to public health.

Correlation of DNA load, genotyping, and clinical phenotype of Mycoplasma pneumoniae infection in children.

This study aimed to investigate the correlation between Mycoplasma pneumoniae (MP)-DNA load in the bronchoalveolar lavage fluid (BALF) of children with MP pneumonia (MPP) and its subtypes, relevant laboratory data, imaging, extrapulmonary complications in infected children, and its clinical significance in evaluating the disease. Children hospitalized with MPP at Tianjin Children's Hospital between December 2017 and December 2020 were selected for the study, excluding those with mixed viral, bacterial, and fungal infections. Children were divided into low- and high-load groups according to the MP DNA load in BALF using real-time quantitative fluorescence polymerase chain reaction (PCR). After a successful MP culture, positive specimens were subjected to PCR-Restriction fragment length polymorphism and Multiple-locus variable number tandem repeat analysis typing. Basic data, clinical information, laboratory data, and radiological results were collected from all children included in the study. The PI-I type dominated the different load groups. Children in the low-load group had more wheezing and shortness of breath; however, children in the high-load group had a higher length of hospitalization, maximum fever temperature, higher chills/chilliness, incidence of abdominal pain, and higher C-reactive protein (CRP), procalcitonin (PCT) and aspartate aminotransferase (AST) levels. Children in the high-load group were more likely to have imaging changes such as pleural effusion, and the incidence of respiratory infections and extrapulmonary complications was higher than that of those in the low-load group. We applied Spearman's correlation analysis to clarify the relationship between MP DNA load and the clinical severity of MPP. We found that MP DNA load was positively correlated with length of hospitalization, maximum fever temperature, CRP, PCT, Interleukin-6 (IL-6), and AST levels, and negatively correlated with fever and cough durations, white blood cell count (WBC), and proportion of monocytes (MONO). The degree of correlation was as follows: length of hospitalization > IL-6 > cough duration > AST > fever duration > PCT > WBC > proportion of MONO > maximum fever temperature > CRP levels. MP DNA load was not correlated with MP typing but was significantly correlated with the children's clinical phenotype. Therefore, the MP DNA load helps in the early diagnosis of infection and can better predict disease regression.

Epidemiological changes and molecular characteristics of Brucella strains in Ningxia, China.

Human brucellosis causes serious public health concerns in Ningxia, China. This study employed epidemiological, bacteriological, and multiple-locus variable-number tandem repeat analysis (MLVA) methods to conduct an epidemiological investigation, which is necessary for devising tailored control strategies. Between 1958 and 2022, 29,892 cases were reported, with an average annual number of cases and incidence of 467 and 7.1/100,000, respectively. The epidemic situation gradually worsened, with cases escalating from 26 cases in 2005 to 6,292 in 2022, with the incidence rate rising from 0.441 in 2005 to 86.83 in 2022. Geographically, the disease spread from a single affected county in 2004 to encompass all 22 counties in 2022. Yanchi County had the highest incidence, followed by the Hongsibao and Tongxin counties. These data suggest that Brucella infection has become a rampant regional concern in human brucellosis. Between 1958 and 2019, a total of 230 Brucella strains were identified across four studied hosts. These strains comprised four species with 12 biovars, including B. melitensis bv. 1, bv. 2, bv. 3, B. abortus bv. 1, bv. 3, bv. 4, bv. 5, bv. 6, bv. 7, B. suis bv. 1 and bv. 3, and B. canis. These data highlight the high species/biovars and host diversity of the Brucella population, posing a substantial challenge to brucellosis surveillance. There was an apparent transition from multiple species/biovars historically to the current dominance of a single species, B. melitensis, emphasizing the requirement for strengthening surveillance of B. melitensis. Genotypes 42 and 116, constituting 96.2% of the total number of genotypes, predominated in panel 1 and MLVA-11, indicating that all strains belong to the East Mediterranean lineage. MLVA cluster analysis revealed persistent transmission of dominant circulating genotypes, presenting an epidemic pattern characterized primarily by epidemiologically related cases with a few sporadic cases. Strains in this study exhibited high genetic homogeneity with strains from the Northwest, and those from Kazakhstan and Mongolia. The epidemic situation of human brucellosis has gradually worsened; the rampant epidemic of the disease has become a regional concern. The present study highlights that implementing the of targeted surveillance and intervention strategies is urge.

Molecular Analysis of Enterococcus Faecalis Isolates in a 4-year Period.

In the present research, we aimed to determine the characteristics of E. faecalis strains collected from an Iranian Children's Hospital for four years. Sixty-seven E. faecalis isolates with virulence genes detection, variable-number tandem repeat (VNTR), and multiple-locus variable-number tandem repeat analysis (MLVA) typing were investigated. A high frequency of virulence genes belonged to gelatinase (73%) and Enterococcus faecalis (62%). The MLVA of 67 E. faecalis isolates revealed 52 VNTR patterns and 38 MLVA types (MTs). Furthermore, genetic diversities with the majority of the MT1 as a major MT in different Wards of the Children's Hospital were found.

The serological and genetic diversity of the Leptospira interrogans Icterohaemorrhagiae serogroup circulating in the UK.

Strains of Leptospira interrogans belonging to two very closely related serovars, Icterohaemorrhagiae and Copenhageni, have been associated with disease in mammalian species and are the most frequently reported agents of human leptospirosis. They are considered the most pathogenic serovars and represent more than half of the leptospires encountered in severe human infections. Nineteen such isolates from the United Kingdom - human, domestic and wildlife species - were typed using three monoclonal antibodies (F12 C3, F70 C14 and F70 C24) in an attempt to elucidate their epidemiology. They were further examined by restriction endonuclease analysis (REA), multiple-locus variable-number tandem repeat analysis (MLVA) and lic12008 gene sequence analysis. Monoclonal antibody F12 C3, which is highly specific for Icterohaemorrhagiae and Copenhageni, confirmed that all the strains belonged to these two serovars. Sixteen strains were identified as Copenhageni and three as Icterohaemorrhagiae serovar. Only one restriction pattern type was identified, thus confirming that REA is not able to discriminate between the Icterohaemorrhagiae and Copenhageni serovars. Variable-number tandem-repeat analysis found three loci with differences in the repeat number, indicating genetic diversity between British isolates. Sequences of the lic12008 gene showed that all isolates identified as the Icterohaemorrhagiae serotype have a single base insertion, in contrast to the same sequences of the Copenhageni serotype. Copenhageni is the predominant serovar in the Icterohaemorrhagiae serogroup isolated in British Isles. There is a genetic diversity of MLVA patterns of the isolates but no genetic tool used in the study was able to determine serovars.

Molecular epidemiology and antimicrobial resistance patterns of carbapenem-resistant Acinetobacter baumannii isolates from patients admitted at ICUs of a teaching hospital in Zunyi, China.

Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a predominant strain of healthcare-associated infections worldwide, particularly in intensive care units (ICUs). Therefore, it is imperative to study the molecular epidemiology of CRAB in the ICUs using multiple molecular typing methods to lay the foundation for the development of infection prevention and control strategies. This study aimed to determine the antimicrobial susceptibility profile, the molecular epidemiology and conduct homology analysis on CRAB strains isolated from ICUs. The sensitivity to various antimicrobials was determined using the minimum inhibitory concentration (MIC) method, Kirby-Bauer disk diffusion (KBDD), and E-test assays. Resistance genes were identified by polymerase chain reaction (PCR). Molecular typing was performed using multilocus sequence typing (MLST) and multiple-locus variable-number tandem repeat analysis (MLVA). Among the 79 isolates collected, they exhibited high resistance tovarious antimicrobials but showed low resistance to levofloxacin, trimethoprim-sulfamethoxazole, and tetracyclines. Notably, all isolates of A. baumannii were identified as multidrug-resistant A. baumannii (MDR-AB). The bla OXA-51-like, adeJ, and adeG genes were all detected, while the detection rates of bla OXA-23-like (97.5%), adeB (93.67%), bla ADC (93.67%), qacEΔ1-sul1 (84.81%) were higher; most of the Ambler class A and class B genes were not detected. MLST analysis on the 79 isolates identified five sequence types (STs), which belonged to group 3 clonal complexes 369. ST1145Ox was the most frequently observed ST with a count of 56 out of 79 isolates (70.89%). MLST analysis for non-sensitive tigecycline isolates, which were revealed ST1145Ox and ST1417Ox as well. By using the MLVA assay, the 79 isolates could be grouped into a total of 64 distinct MTs with eleven clusters identified in them. Minimum spanning tree analysis defined seven different MLVA complexes (MCs) labeled MC1 to MC6 along with twenty singletons. The locus MLVA-AB_2396 demonstrated the highest Simpson's diversity index value at 0.829 among all loci tested in this study while also having one of the highest variety of tandem repeat species. The molecular diversity and clonal affinities within the genomes of the CRAB strains were clearly evident, with the identification of ST1144Ox, ST1658Ox, and ST1646Oxqaq representing novel findings.

Prevalence and genetic distribution of Legionella spp. in public bath facilities in Kobe City, Japan.

Legionella is an important waterborne pathogen that causes legionellosis. Public baths are considered the primary cause of legionellosis infection in Japan. We investigated the prevalence and genetic distribution of 338 Legionella spp. isolates from 81 public bath facilities, including 35 hot springs and 46 other facilities, through annual periodic surveillance in Kobe, Japan, from 2016 to 2021. In addition, the genotypes of nine clinical strains of unknown infectious source from the same period were compared to those of bathwater isolates. We elucidated the differences in the distribution of Legionella species, serogroups, and genotypes between hot springs and other public baths. Legionella israelensis, L. londiniensis, and L. micdadei colonized hot springs along with L. pneumophila. The minimum spanning tree analysis based on multiple-locus variable number tandem repeat analysis (MLVA) also identified four major clonal complexes (CCs) in L. pneumophila SG1 and found that CC1 of the four CCs is a specific novel genotype with the lag-1 gene in hot springs. The same MLVA genotypes and sequence types as those of the clinical strains were not present among the strains isolated from bath water. Thus, our surveillance is useful for estimating the sources of legionellosis infection in Japan and developing prevention strategies.

Characterization of integrons, extended spectrum beta lactamases and genetic diversity among uropathogenic Escherichia coli isolates from Kerman, south east of Iran.

The study aimed to investigate the distribution of genes encoding integrons, extended spectrum beta-lactamase (ESBL) in E. coli isolated from UTIs, as well as the genetic diversity among the isolates. E. coli isolates were recovered from the patients with UTI in Kerman Iran. Antibiotic susceptibility was done according to CLSI guidelines. The presence of ESBL genes and integrons was evaluated using PCR. PCR and sequencing were applied for the evaluation of cassette content of integrons. Genotyping of the isolates was performed by multiple-locus variable-number tandem repeat analysis (MLVA). Imipenem was the most effective antibiotic, while the highest resistance was observed to streptomycin. In total 40.2% of isolates were ESBL producers. Of 69 integron-positive isolates, 59 only had class I integrons, 4 only had class II integrons and 6 had both types. The most common gene cassette found within class I integrons was dfrA17-aadA5 (n=27). The E. coli isolates were divided into 16 MLVA clusters. The current study demonstrated the simultaneous presence of class I integrons and ESBLs involved in the resistance of UPEC isolates to antibacterial agents. Our finding also revealed that the E. coli isolates belonged to diverse clones.

Characterization of quinolone resistance in Salmonella enterica serovar Typhimurium and its monophasic variants from food and patients in China

The study aimed to characterize the quinolone resistance of Salmonella enterica serovar Typhimurium and its monophasic variant (Salmonella enterica serovar 1,4,[5],12:i:-) isolated from food and patients in China. All of the isolates were assessed for quinolone susceptibility via the broth microdilution method. Then, the isolates were checked for mutations within quinolone resistance-determining regions of gyrA, gyrB, parC, and parE and were examined for plasmid-mediated quinolone resistance genes. High rates of resistance to nalidixic acid in the S. Typhimurium (70.7%) and S. 1,4,[5],12:i:- (41.9%) isolates were observed, and a considerable proportion of isolates with reduced susceptibility to ciprofloxacin and levofloxacin were also detected. The high frequency of mutations in GyrA (60.8%) and a variety of genes (aac[6']-Ib-cr [23.2%], oqxAB [19.2%], qnrS [13.6%], and qnrA [3.2%]) conferring quinolone resistance in these Salmonella isolates were noteworthy. Lastly, the isolates carrying qnrS for transferability and transmission of the quinolone resistance were analysed by conjugation. Multiple locus variable-number tandem repeat analysis profiles indicated that some qnrS-positive isolates were clonally related, whilst the other isolates were genetically divergent. This suggested that both clonal spread of resistant strains and horizontal transmission of the plasmid-mediated resistance genes contributed to the dissemination of qnrS-positive Salmonella isolates. This study highlights the prevalence of quinolone-resistant S. Typhimurium and S. 1,4,[5],12:i:- in China, posing a threat to public health.