Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Typhi.

Background: Typhoid fever results from systemic infection with serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccination) and effective antimicrobial treatment. Antimicrobial resistant (AMR) Typhi lineages have emerged and become established in many parts of the world.

Genomic and pathogenicity analyses to identify the causative agent from multiple serogroups of non-O1, non-O139 in foodborne outbreaks.

In 2013, foodborne outbreaks in Japan were linked to non-O1, non-O139 . However, laboratory tests have detected several serogroups, making it difficult to determine the causative agent. Therefore, whole-genome analyses revealed that only serogroup O144 possesses a genomic island with a type III secretion system (T3SS).

Genomic perspective on the bacillus causing paratyphoid B fever.

Paratyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). However, little was known about the global population structure, geographic distribution, and evolution of this pathogen. Here, we report a whole-genome analysis of 568 historical and contemporary SPB PG1 isolates, obtained globally, between 1898 and 2021.

Characterization of in northern Vietnam in 2012-2016.

Introduction: Shigellosis remains a considerable public health concern in developing countries. and are prevalent worldwide and has been replacing .

Gap Statement: still causes outbreaks of shigellosis in northern Vietnam but limited information is available on its genetic characteristics.

Epidemiologic and genomic investigations of an unusual increase in Salmonella enterica serovar Paratyphi A infection among travelers returning from Myanmar in 2015.

Objectives: An unusual increase in Salmonella enterica serovar Paratyphi A infection rate in Japanese travelers returning from Myanmar was observed in 2015.

Methods: We analyzed epidemiologic data of returned travelers with enteric fever from 2005-2019. We also analyzed 193 Salmonella Paratyphi A isolates, including 121 isolates with published genomes.

Multijurisdictional Outbreak of Enterohemorrhagic O157 Caused by Consumption of Ready-to-Eat Grilled Skewered Meat in Niigata, Japan.

Enterohemorrhagic O157 (EHEC) causes severe complications such as hemolytic uremic syndrome. Contaminated ready-to-eat (RTE) food is one of the vehicles of multijurisdictional outbreaks of foodborne disease worldwide. Multijurisdictional (covering cities, towns, and villages) outbreaks of EHEC are usually linked to an increase in cases, and here we describe such an outbreak involving 29 cases in October 2017 in the Niigata Prefecture.

Corrigendum to: Phylogenetic Analysis Revealed the Dissemination of Closely Related Epidemic O1 Isolates in Laos, Thailand, and Vietnam.

[This corrects the article DOI: 10.1093/ofid/ofaa492.].

Molecular characterization of O1 isolates obtained from outbreaks in the Philippines, 2015-2016.

The Philippines, comprising three island groups, namely, Luzon, Visayas and Mindanao, experienced an increase in cholera outbreaks in 2016. Previous studies have shown that isolates obtained from the Philippines are novel hybrid El Tor strains that have evolved in the country and are clearly distinct from those found in Mozambique and Cameroon. The characterization of the strains isolated from outbreaks has been limited to phenotypic characteristics, such as biochemical and serological characteristics, in most previous studies.

Multilocus Variable-Number Tandem-Repeat Analysis of Enterohemorrhagic Serogroups O157, O26, and O111 Based on a Look-Up Table Constructed by Regression Analysis.

Multilocus variable-number tandem-repeat analysis (MLVA) is a widely accepted molecular typing tool for enterohemorrhagic (EHEC). However, ensuring the accuracy of MLVA data among multiple laboratories remains difficult. We developed a method of constructing adjusted look-up tables, which are necessary for MLVA profiling, at each laboratory using a regression analysis based on electrophoresis data from 24 in-house reference strains.

Phylogenetic Analysis Revealed the Dissemination of Closely Related Epidemic O1 Isolates in Laos, Thailand, and Vietnam.

We performed whole-genome sequencing of O1 isolates from Laos, Thailand, and Vietnam, where cholera outbreaks occurred, to determine their genetic lineages. Core genome phylogenetic analysis revealed that the isolates located in same lineage without regional clusters, which suggests that closely related strains circulated in Southeast Asia.

Whole-Genome Analysis of Clinical Vibrio cholerae O1 in Kolkata, India, and Dhaka, Bangladesh, Reveals Two Lineages of Circulating Strains, Indicating Variation in Genomic Attributes.

serogroup O1 is responsible for epidemic and pandemic cholera and remains a global public health threat. This organism has been well established as a resident flora of the aquatic environment that alters its phenotypic and genotypic attributes for better adaptation to the environment. To reveal the diversity of clinical isolates of O1 in the Bay of Bengal, we performed whole-genome sequencing of isolates from Kolkata, India, and Dhaka, Bangladesh, collected between 2009 and 2016.

Multilocus sequence typing reveals diverse known and novel genotypes of Leptospira spp. circulating in Sri Lanka.

Background: Leptospirosis has gained much attention in Sri Lanka since its large outbreak in 2008. However, most of the cases were clinically diagnosed and information on Leptospira genotypes and serotypes currently prevailing in the country is lacking.

Methodology/principal Findings: We retrospectively analyzed 24 Leptospira strains from human patients as well as isolated and characterized three Leptospira strains from black rats using the microscopic agglutination test with antisera for 19 serovars and multilocus sequence typing.

Genetic relatedness of Leptospira interrogans serogroup Autumnalis isolated from humans, dogs, and mice in Japan.

Objective: Leptospirosis is a zoonotic disease caused by pathogenic spirochetes of Leptospira spp., and peridomiciliary rodents are the most important reservoir animals for human infection. Dogs are known to be the reservoir animal of L.

A shigellosis outbreak associated with a sports festival at a kindergarten in Kitakyushu City, Japan.

Introduction: Shigellosis cases have decreased gradually in Japan in recent years, but indigenous shigellosis outbreaks sometimes occur in childcare facilities. From national surveillance data, we identified a shigellosis outbreak involving a kindergarten.

Methods: After detecting Shigella sonnei in Kitakyushu City, we conducted active case finding and epidemiological investigation in Kindergarten Z, including stool specimen collection and interviews.

Multiple-Locus Variable-Number Tandem Repeat Analysis Scheme for Non-O157 Shiga Toxin-Producing Escherichia coli: Focus on Serogroups O103, O121, O145, O165, and O91.

Non-O157 Shiga toxin-producing Escherichia coli (STEC) infections are a growing concern for public health. The number of sporadic cases and outbreaks of non-O157 STEC infections have increased in recent years. Molecular subtyping is an essential tool that allows high-resolution and rapid differentiation of isolates, identification of case clusters, and detection of outbreak clusters.

Bacteremia Caused by Salmonella Poona in a Healthy Adult in Tokyo, Japan.

Non-typhoidal Salmonella (NTS) infection is a major pathogen causing gastroenteritis among immunocompetent adults. NTS infection is mainly transmitted by contaminated food and water, but some cases are transmitted by animal contact. Salmonella enterica subsp.

Genome Sequence of a Salmonella enterica Serotype Senftenberg Strain Lacking Pathogenicity Island-1 and Isolated in Japan.

We report here the genome sequence of a serotype Senftenberg strain, isolated from feather meal, in which the pathogenicity island-1 was deleted.

Molecular analysis of virulence factors of hypermucoviscous Klebsiella pneumoniae in a diabetes patient with multifocal intramuscular and musculoskeletal abscesses.

Unusual community-acquired invasive Klebsiella pneumoniae infection has been reported worldwide, particularly in Asia. Recently, several virulence-associated genes of the isolates have been investigated. We report a case of multifocal intramuscular and musculoskeletal abscesses caused by K.

Effective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157.

Due to the potential of enterohemorrhagic (EHEC) serogroup O157 to cause large food borne outbreaks, national and international surveillance is necessary. For developing an effective method of molecular surveillance, a conventional method, multilocus variable-number tandem-repeat analysis (MLVA), and whole-genome sequencing (WGS) analysis were compared. WGS of 369 isolates of EHEC O157 belonging to 7 major MLVA types and their relatives were subjected to comprehensive typing, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) analyses.

Vibrio cholerae Infection in Japan Not Associated with Overseas Travel.

A 74-year-old Japanese man who was taking antacids presented with profuse diarrhea. Stool culture revealed Vibrio cholerae O1 strain, serogroup Ogawa, biotype El tor. He recalled he had consumed some sashimi but denied any history of travelling abroad, and another cholera case with almost the same strain was reported at the same time in a remote prefecture in the Kanto area.

Development of a loop-mediated isothermal amplification assay for Vibrio cholerae O1 and O139.

A loop-mediated isothermal amplification assay was developed. It was designed for recognizing Vibrio cholerae O1/O139, where atpA, rfbN, and wfbR genes were adopted. The assay specifically detected the target with sensitivities of 5-67 copies per reaction in 1 h.