Clonal expansion of chromosome-borne CTX-M-55 extended-spectrum β-lactamase-producing serovar Agona, Taiwan.

We investigated emerging multidrug-resistant (MDR) serovar Agona in Taiwan. These MDR strains commonly harbored the efflux pump activator gene and up to 15 resistance genes, including , , , , , , , , , , ), , , , and ), within IncHI2-IncHI2A plasmids or diverse chromosomal resistance genomic islands (RGIs). These newly emerging MDR strains comprised 44.

Prevalence and Virulence Profiles of Klebsiella pneumoniae Isolated From Different Animals.

Background: Klebsiella pneumoniae liver abscess (KLA) is an invasive disease, and the occurrence of infection is related to its virulence factors and colonization of the host's gastrointestinal (GI) tract. Some animal-sourced isolates share virulence factors with human pathogens. However, the potential of K.

The rise in domestic shigellosis and the genomic characteristics of clones linked to men who have sex with men in Taiwan, 2015‒2022.

Unlabelled: Since 2015, Taiwan has experienced a notable rise in domestic shigellosis cases, particularly among young adult males. In this study, we aimed to investigate this epidemiological trend through demographic analysis and genomic characterization of bacterial isolates. We analyzed demographic data on shigellosis cases from 2003-2014 to 2015-2022.

Antimicrobial resistance and genetic relatedness among Campylobacter coli and Campylobacter jejuni from humans and retail chicken meat in Taiwan.

Objectives: Campylobacter is a significant zoonotic pathogen primarily transmitted through poultry. Our study aimed to assess antimicrobial resistance and genetic relationships among Campylobacter isolates from retail chicken meat and humans in Taiwan.

Methods: Campylobacter isolates were analysed using whole-genome sequencing to investigate their antimicrobial resistance, genetic determinants of resistance, and genotypes.

The usefulness of nanopore sequencing in whole-genome sequencing-based genotyping of and serovar Enteritidis.

Unlabelled: Bacterial genotyping through whole-genome sequencing plays a crucial role in disease surveillance and outbreak investigations in public health laboratories. This study assessed the effectiveness of Oxford Nanopore Technologies (ONT) sequencing in the genotyping of and serovar Enteritidis. Our results indicated that ONT sequences, generated with the R10.

Epidemiological trends in serotypes distribution and antimicrobial resistance in from humans in Taiwan, 2004-2022.

Objectives: , a zoonotic pathogen, significantly impacts global human health. Understanding its serotype distribution and antimicrobial resistance is crucial for effective control measures and medical interventions.

Methods: We collected isolates and demographic data from Taiwanese hospitals between 2004 and 2022, analyzing their serotypes and antimicrobial susceptibility.

Distinct evolution of ST11 KL64 in Taiwan.

Carbapenem-resistant ST11_KL64 emerged as a significant public health concern in Taiwan, peaking between 2013 and 2015, with the majority of isolates exhibiting OXA-48 as the sole carbapenemase. In this study, we employed whole-genome sequencing to investigate the molecular underpinnings of ST11_KL64 isolates collected from 2013 to 2021. Phylogenomic analysis revealed a notable genetic divergence between the ST11_KL64 strains in Taiwan and those in China, suggesting an independent evolutionary trajectory.

Correcting modification-mediated errors in nanopore sequencing by nucleotide demodification and reference-based correction.

The accuracy of Oxford Nanopore Technology (ONT) sequencing has significantly improved thanks to new flowcells, sequencing kits, and basecalling algorithms. However, novel modification types untrained in the basecalling models can seriously reduce the quality. Here we reports a set of ONT-sequenced genomes with unexpected low quality due to novel modification types.

Shigellosis in Taiwan: An old enteric pathogen with changing epidemiology and increasing antimicrobial resistance.

While the incidence of shigellosis has decreased in developed nations due to improved living conditions and healthcare systems, it remains prevalent in economically developing regions. In recent years, a resurgence of shigellosis has been observed in the United States, Europe, and Taiwan, primarily among men having sex with men and people living with human immunodeficiency virus, along with a rise in antimicrobial resistance. This study aims to review the historical epidemiological trends and drug resistance in shigellosis, with a focus on Taiwan.

Carbapenem resistance in extensively drug-resistant serovar Agona and AmpC β-lactamase-producing Infantis.

Carbapenem resistance arising from the loss of porins is commonly observed in extended-spectrum β-lactamase (ESBL) and AmpC β-lactamase-producing strains of certain genera, including , , and . However, this resistance mechanism is rarely reported in the genus. To address this knowledge gap, our study offers genetic evidence demonstrating that the loss of two specific porins (OmpC_378 and OmpD) is crucial for the development of carbapenem resistance in ESBL and AmpC β-lactamase-producing strains.

Epidemiological trends and antimicrobial resistance in Salmonella enterica serovar Typhimurium clones in Taiwan between 2004 and 2019.

Objectives: We investigated the temporal trends of Salmonella enterica serovar Typhimurium (S. Typhimurium) clones in Taiwan from 2004 to 2019, focusing on antimicrobial resistance (AMR), resistance genetic determinants, and plasmid types.

Methods: Salmonella isolates were characterized using pulsed-field gel electrophoresis (PFGE), whole-genome sequencing, and antimicrobial susceptibility testing.

Chromosome-Borne CTX-M-65 Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serovar Infantis, Taiwan.

A CTX-M-65‒producing Salmonella enterica serovar Infantis clone, probably originating in Latin America and initially reported in the United States, has emerged in Taiwan. Chicken meat is the most likely primary carrier. Four of the 9 drug resistance genes have integrated into the chromosome: bla, tet(A), sul1, and aadA1.

Antimicrobial Resistance and Mechanisms of Azithromycin Resistance in Nontyphoidal Salmonella Isolates in Taiwan, 2017 to 2018.

Antimicrobial resistance was investigated in 2,341 nontyphoidal Salmonella (NTS) isolates recovered from humans in Taiwan from 2017 to 2018 using antimicrobial susceptibility testing. Azithromycin resistance determinants were detected in 175 selected isolates using PCR and confirmed in 81 selected isolates using whole-genome sequencing. Multidrug resistance was found in 47.

Genomic Surveillance of Listeria monocytogenes in Taiwan, 2014 to 2019.

Listeria monocytogenes is a life-threatening foodborne pathogen. Here, we report the genomic characterization of a nationwide dataset of 411 clinical and 82 food isolates collected in Taiwan between 2014 and 2019. The observed incidence of listeriosis increased from 0.

Microevolution of CG23-I Hypervirulent Klebsiella pneumoniae during Recurrent Infections in a Single Patient.

CG23-I lineage constitutes the majority of hypervirulent Klebsiella pneumoniae. A diabetic patient suffered six episodes of infections caused by CG23-I K. pneumoniae.

Demographic Features of Invasive Meningococcal Disease in Taiwan, 1993 to 2020, and Genetic Characteristics of Neisseria meningitidis Isolates, 2003 to 2020.

We present the demographic features of invasive meningococcal disease (IMD) in Taiwan between 1993 and 2020 and the genetic characteristics of Neisseria meningitidis isolates recovered from 2003 to 2020. IMD was rare in Taiwan between 1993 and 2020, with an annual incidence ranging from 0.009 to 0.

A nosocomial salmonellosis outbreak caused by bla-carrying, extensively drug-resistant Salmonella enterica serovar Goldcoast in a hospital respiratory care ward in Taiwan.

Objectives: A nosocomial salmonellosis outbreak caused by Salmonella enterica serovar Goldcoast occurred in a respiratory care ward (RCW) of a hospital in central Taiwan between December 24, 2020, and January 21, 2021. Ten isolates recovered from 10 RCW residents were resistant to extended-spectrum cephalosporins. The resistance mechanism needs to be investigated.

Association between Escherichia coli with NotI-restriction resistance and urinary tract infections.

Background: Escherichia coli is the most common cause of urinary tract infections (UTIs). It is widely accepted that uropathogenic E. coli (UPEC) mainly emerge from the distal gut microbiota.

Antimicrobial Resistance in Campylobacter coli and Campylobacter jejuni from Human Campylobacteriosis in Taiwan, 2016 to 2019.

Campylobacter coli and Campylobacter Jejuni are highly resistant to most therapeutic antimicrobials in Taiwan; rapid diagnostics of resistance in bacterial isolates is crucial for the treatment of campylobacteriosis. We characterized 219 (40 C. coli and 179 C.

RamAp Is an Efflux Pump Regulator Carried by an IncHI2 Plasmid.

In investigating the epidemiological trends of Salmonella enterica serovar Goldcoast, we previously identified several closely related strains with different MICs to azithromycin and quinolones. Genome sequencing and comparison of two very similar multidrug-resistant (MDR) strains, R18.0877 and R18.

Two ST11 strains exacerbate colorectal tumorigenesis in a colitis-associated mouse model.

Sequence type (ST) 11 is one of the major lineages of carbapenem-resistant (CRKP). Although the gastrointestinal (GI) carriage of CRKP predisposes individuals to subsequent infections, little is known for its impact on gut homeostasis. In this study, we investigated the association between ST11 CRKP colonization and colorectal cancer (CRC).

Assessment of metrics in next-generation sequencing experiments for use in core-genome multilocus sequence type.

With the reduction in the cost of next-generation sequencing, whole-genome sequencing (WGS)-based methods such as core-genome multilocus sequence type (cgMLST) have been widely used. However, gene-based methods are required to assemble raw reads to contigs, thus possibly introducing errors into assemblies. Because the robustness of cgMLST depends on the quality of assemblies, the results of WGS should be assessed (from sequencing to assembly).