Mycobacterium tuberculosis lineage: a naming of the parts

There have been many reports of groups of related Mycobacterium tuberculosis strains described variously as lineages, families or clades. There is no objective definition of these groupings making it impossible to define relationships between those groups with biological advantages. Here we describe two groups of related strains obtained from an epidemiological study in Tanzania which we define as the Kilimanjaro and Meru lineages on the basis of IS6110 restriction fragment length polymorphism (RFLP), polymorphic GC rich sequence (PGRS) RFLP and mycobacterial interspersed repeat unit (MIRU) typing. We investigated the concordance between each of the typing techniques and the dispersal of the typing profiles from a core pattern. The Meru lineage is more dispersed than the Kilimanjaro lineage and we speculate that the Meru lineage is older. We suggest that this approach provides an objective definition that proves robust in this epidemiological study. Such a framework will permit associations between a lineage and clinical or bacterial phenomenon to be tested objectively. This definition will also enable new putative lineages to be objectively tested

An overview of the evolution of infrared spectroscopy applied to bacterial typing

The sustained emergence of new declared bacterial species makes typing a continuous challenge for microbiologists. Molecular biology techniques have a very significant role in the context of bacterial typing, but they are often very laborious, time consuming and eventually fail when dealing with very closely related species. Spectroscopic-based techniques appear in some situations as a viable alternative to molecular methods with advantages in terms of analysis time and cost. Infrared and mass spectrometry are among the most exploited techniques in this context: particularly, infrared spectroscopy emerged as a very promising method with multiple reported successful applications. This article presents a systematic review on infrared spectroscopy applications for bacterial typing, highlighting fundamental aspects of infrared spectroscopy, a detailed literature review (covering different taxonomic levels and bacterial species), advantages and limitations of the technique over molecular biology methods and a comparison with other competing spectroscopic techniques such as MALDI-TOF MS, Raman and intrinsic fluorescence. Infrared spectroscopy possesses a high potential for bacterial typing at distinct taxonomic levels and worthy of further developments and systematization. The development of databases appears fundamental towards the establishment of infrared spectroscopy as a viable method for bacterial typing.FCT -Fundação para a Ciência e a Tecnologia(PT2020 UID/QUI/50006/2013)info:eu-repo/semantics/publishedVersio

Use of whole-genus genome sequence data to develop a multilocus sequence typing tool that accurately identifies Yersinia isolates to the species and subspecies levels

The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica

Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis

Background: Following the association of Cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the World Health Organization (WHO) in 2004 requested the establishment of a molecular typing scheme to enable the international control of the organism. This paper presents the application of Next Generation Sequencing (NGS) to Cronobacter which has led to the establishment of the Cronobacter PubMLST genome and sequence definition database (http://pubmlst.org/ cronobacter/) containing over 1000 isolates with metadata along with the recognition of specific clonal lineages linked to neonatal meningitis and adult infections Results: Whole genome sequencing and multilocus sequence typing (MLST) has supports the formal recognition of the genus Cronobacter composed of seven species to replace the former single species Enterobacter sakazakii. Applyingthe 7-loci MLST scheme to 1007 strains revealed 298 definable sequence types, yet only C. sakazakii clonal complex 4 (CC4) was principally associated with neonatal meningitis. This clonal lineage has been confirmed using ribosomal-MLST (51-loci) and whole genome-MLST (1865 loci) to analyse 107 whole genomes via the Cronobacter PubMLST database. This database has enabled the retrospective analysis of historic cases and outbreaks following re-identification of those strains. Conclusions: The Cronobacter PubMLST database offers a central, open access, reliable sequence-based repository for researchers. It has the capacity to create new analysis schemes 'on the fly', and to integrate metadata (source, geographic distribution, clinical presentation). It is also expandable and adaptable to changes in taxonomy, and able to support the development of reliable detection methods of use to industry and regulatory authorities. Therefore it meets the WHO (2004) request for the establishment of a typing scheme for this emergent bacterial pathogen. Whole genome sequencing has additionally shown a range of potential virulence and environmental fitness traits which may account for the association of C. sakazakii CC4 pathogenicity, and propensity for neonatal CNS

Evaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis

Background: Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation. Methods: Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively. Results: Single nucleotide polymorphism (SNP)-based cluster analysis of Salmonella Typhimurium genomes revealed well supported clades, that were concordant with epidemiologically defined outbreak and confirmed the source of outbreak is due to consumption of contaminated mayonnaise. SNP-analyses of Salmonella Dublin genomes confirmed the outbreak however the source of infection could not be determined. The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could neither discriminate between the outbreak and non-outbreak strains of Salmonella Typhimurium nor confirm that contaminated mayonnaise is the source of infection, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory and could not confirm the source of the outbreak. Conclusions: Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. In this study, we showed that SNP-based analyses do not only have the ability to confirm the occurrence of the outbreak but also to provide definitive evidence of the source of the outbreak in real-time

Diversity and Dynamics of Indigenous \u3cem\u3eRhizobium japonicum\u3c/em\u3e Populations

A simple method, based upon the separation of cellular proteins by sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis, has been devised for distinguishing between isolates of Rhizobium japonicum. Eleven laboratory strains, previously classified into five serogroups, were analyzed by gel electrophoresis. Groups determined subjectively according to protein patterns matched the serogroups, with one exception. Most strains within serogroups could be distinguished from one another. For studying the ecology of Rhizobium, an important advantage of this technique compared with serology or phage typing is that it discriminates among previously unencountered indigenous bacterial isolates as well as among known laboratory strains. SDS-gels were used to analyze the Rhizobium population of 500 nodules, sampled throughout the growing season, from soybeans at two different Wisconsin localities. Although the soybeans had been inoculated with laboratory strains of R. japonicum, indigenous R. japonicum predominated. At one location, 19 indigenous gel types were distinguished and classified mainly into four groups. At the other location, 18 gel types, falling mainly into three groups, were detected. The predominance of a particular group varied, in some cases dramatically, depending upon the time and depth of nodule formation

Status and potential of bacterial genomics for public health practice : a scoping review

Background: Next-generation sequencing (NGS) is increasingly being translated into routine public health practice, affecting the surveillance and control of many pathogens. The purpose of this scoping review is to identify and characterize the recent literature concerning the application of bacterial pathogen genomics for public health practice and to assess the added value, challenges, and needs related to its implementation from an epidemiologist’s perspective. Methods: In this scoping review, a systematic PubMed search with forward and backward snowballing was performed to identify manuscripts in English published between January 2015 and September 2018. Included studies had to describe the application of NGS on bacterial isolates within a public health setting. The studied pathogen, year of publication, country, number of isolates, sampling fraction, setting, public health application, study aim, level of implementation, time orientation of the NGS analyses, and key findings were extracted from each study. Due to a large heterogeneity of settings, applications, pathogens, and study measurements, a descriptive narrative synthesis of the eligible studies was performed. Results: Out of the 275 included articles, 164 were outbreak investigations, 70 focused on strategy-oriented surveillance, and 41 on control-oriented surveillance. Main applications included the use of whole-genome sequencing (WGS) data for (1) source tracing, (2) early outbreak detection, (3) unraveling transmission dynamics, (4) monitoring drug resistance, (5) detecting cross-border transmission events, (6) identifying the emergence of strains with enhanced virulence or zoonotic potential, and (7) assessing the impact of prevention and control programs. The superior resolution over conventional typing methods to infer transmission routes was reported as an added value, as well as the ability to simultaneously characterize the resistome and virulome of the studied pathogen. However, the full potential of pathogen genomics can only be reached through its integration with high-quality contextual data. Conclusions: For several pathogens, it is time for a shift from proof-of-concept studies to routine use of WGS during outbreak investigations and surveillance activities. However, some implementation challenges from the epidemiologist’s perspective remain, such as data integration, quality of contextual data, sampling strategies, and meaningful interpretations. Interdisciplinary, inter-sectoral, and international collaborations are key for an appropriate genomics-informed surveillance

Molecular Genetic Typing of Staphylococcus aureus from Cows, Goats, Sheep, Rabbits and Chickens

End of project reportsS. aureus can also cause a number of infections in animals such as tick-associated pyaemia in lambs, staphylococcosis in rabbits, septicaemia, abscesses and chondronecrosis in chickens and pneumonia and osteomyelitis complex in turkeys. S. aureus is the most frequent cause of bovine mastitis, a disease that is of economic importance worldwide (Beck et al., 1992). Typically staphylococcal mastitis is chronic in nature, with subclinical mastitis being the most common form

Multilocus sequence typing of Cronobacter spp. from powdered infant formula and milk powder production factories

This study applied the Cronobacter spp. multilocus sequence typing (MLST) scheme to three strain collections, then known as Enterobacter sakazakii, which had been isolated between 1988 and 2009 from 14 countries. The results revealed the predominance (85%) of C. 29 sakazakii (72 strains) in all three collections. The remaining strains were C. turicensis (10%), C. malonaticus (4%), and C. muytjensii (1%). No strains of C. dublinensis, C. universalis or C. condimenti were identified. Twenty-one out of seventy two C. sakazakii strains were in the clinically significant ST4 clonal complex, and were found in all three strain collections. These results confirm C. sakazakii ST4 is one of the predominant clonal complexes over the past 20 years in several parts of the world. Further understanding of the ecosystem and sources of the organism may be used for the development of improved intervention strategies in the dairy industry