Together with plague, smallpox and typhus, epidemics of dysentery have been a major scourge of human populations for centuries(1). A previous genomic study concluded that Shigella dysenteriae type 1 (Sd1), the epidemic dysentery bacillus, emerged and spread worldwide after the First World War, with no clear pattern of transmission(2). This is not consistent with the massive cyclic dysentery epidemics reported in Europe during the eighteenth and nineteenth centuries(1,3,4) and the first isolation of Sd1 in Japan in 1897(5). Here, we report a whole-genome analysis of 331 Sd1 isolates from around the world, collected between 1915 and 2011, providing us with unprecedented insight into the historical spread of this pathogen. We show here that Sd1 has existed since at least the eighteenth century and that it swept the globe at the end of the nineteenth century, diversifying into distinct lineages associated with the First World War, Second World War and various conflicts or natural disasters across Africa, Asia and Central America. We also provide a unique historical perspective on the evolution of antibiotic resistance over a 100-year period, beginning decades before the antibiotic era, and identify a prevalent multiple antibiotic-resistant lineage in South Asia that was transmitted in several waves to Africa, where it caused severe outbreaks of disease.

Serotyping is the long-standing gold standard method to determine E. coli H antigens; however, this method requires a panel of H-antigen specific antibodies and often culture-based induction of the H-antigen flagellar motility. In this study, a rapid and accurate method to isolate and identify the Escherichia coli (E. coli) H flagellar antigen was developed using membrane filtration and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Flagella were isolated from pure culture, digested with trypsin, and then subjected to LC-MS/MS using one of two systems (Agilent-nano-LC-QSTAR XL or Proxeon-nano-LC-LTQ-Orbitrap XL). The resulting peptide sequence data were searched against a custom E. coli flagella/H antigen database. This approach was evaluated using flagella isolated from reference E. coli strains representing all 53 known H antigen types and 41 clinical E. coli strains. The resulting LC-MS/MS classifications of H antigen types (MS-H) were concordant with the known H serogroup for all 53 reference types, and of 41 clinical isolates tested, 38 (92.7%) were concordant with the known H serogroup. MS-H clearly also identified two clinical isolates (4.9%) that were untypeable by serotyping. Notably, successful detection and classification of flagellar antigens with MS-H did not generally require induction of motility, establishing this proteomic approach as more rapid and cost-effective than traditional methods, while providing equitable specificity for typing E. coli H antigens.

T raditional methods of phenotyping Escherichia coli bacteria include the serotyping of surface O antigens (lipopolysaccharides), capsule K antigens, and H antigens found on the bacteria's flagellar filaments (1). Despite their usefulness, these conventional antibody-based assays can be costly and laborious to perform due to the wide-ranging quality of antibodies (serum) and the number of antibody agglutination reactions needed to assign a final classification (2, 3). H serotyping is further lengthened by the motility induction required before typing among many distinctive flagellar antigens (H1 to H56; designations H13, H22, and H50 are no longer in use [2,3]).Molecular typing methods using PCR-based amplification and genetic sequencing are gaining popularity for serotype classifications of E. coli due to their potential for high throughput and accuracy (4, 5). Problems with this approach, however, arise because genetics do not necessarily indicate phenotypes and because multiple primers need to be used for amplifying the sequences of unknown antigens. Matrix-associated laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) usage for whole-bacterial-protein profiling to classify and type bacteria has also shown some promising results due to its ease of use and highthroughput potential (6, 7). This platform can currently produce data for some successful bacterial subtyping at the species level but hardly the strain level (i.e., the H and O antigen levels [8]).Recently, we reported a new approach called MS-H for H typing E. coli by purifying and digesting E. coli flagella of reference strains of all 53 known H types on a 0.22-m-pore-size filter membrane, followed by online liquid chromatography-tandem mass spectrometry (LC-MS/MS) of the resulting flagellin peptides. The H-antigen serogroups from flagellin peptide data were identified using a minimum of two sequence-specific peptides (9), and MS-H types were assigned as the top-scoring hit in the identified protein list possessing the highest confidence score (10). An example of data output is shown in Fig. S1 in the supplemental material. This novel approach is thoroughly evaluated here by using 127 clinical isolates, including both motile and nonmotile strains collected from three provinces in Canada over the 1-year period of 2012, and by employing a standardized high-throughput method. The evaluation process comprises two steps: preliminary tests and confirmation assays. Preliminary tests were conducted using both the previously described MS-H typing method and the ISO-certified serotyping method in parallel (10). Rather than testing samples of known H types one by one, however, MS-H was conducted in a blind, high-throughput, batch-by-batch mode in order to replicate the clinical-sample scenario. In the absence of motility induction, flagella of 8 isolates of unknown motilities per batch were extracted and digested, together with 2 reference strains of known H types as control samples. Flagellar peptide sequence data were searched against...

i Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has gained popularity in recent years for rapid bacterial identification, mostly at the genus or species level. In this study, a rapid method to identify the Escherichia coli flagellar antigen (H antigen) at the subspecies level was developed using a MALDI-TOF MS platform with high specificity and sensitivity. Flagella were trapped on a filter membrane, and on-filter trypsin digestion was performed. The tryptic digests of each flagellin then were collected and analyzed by MALDI-TOF MS through peptide mass fingerprinting. Sixty-one reference strains containing all 53 H types and 85 clinical strains were tested and compared to serotyping designations. Wholegenome sequencing was used to resolve conflicting results between the two methods. It was found that DHB (2,5-dihydroxybenzoic acid) worked better than CHCA (␣-cyano-4-hydroxycinnamic acid) as the matrix for MALDI-TOF MS, with higher confidence during protein identification. After method optimization, reference strains representing all 53 E. coli H types were identified correctly by MALDI-TOF MS. A custom E. coli flagellar/H antigen database was crucial for clearly identifying the E. coli H antigens. Of 85 clinical isolates tested by MALDI-TOF MS-H, 75 identified MS-H types (88.2%) matched results obtained from traditional serotyping. Among 10 isolates where the results of MALDI-TOF MS-H and serotyping did not agree, 60% of H types characterized by whole-genome sequencing agreed with those identified by MALDI-TOF MS-H, compared to only 20% byserotyping. This MALDI-TOF MS-H platform can be used for rapid and cost-effective E. coli H antigen identification, especially during E. coli outbreaks. Escherichia coli food contamination can have serious consequences, such as hemolytic-uremic syndrome (HUS) (1, 2), with the 2011 Germany E. coli outbreak presenting a clear example (3). Therefore, the fast identification and typing of E. coli is important for tracking sources of contamination and reducing health risks. Traditional typing of E. coli is based mainly on two surface antigens of the bacteria for antiserum-based agglutination reactions: lipopolysaccharide (LPS) or O antigens for O typing and flagellar proteins or H antigens for H typing (4). The procedure for performing serotyping is time-consuming (2 to 12 days) and barely meets the need for fast diagnosis in outbreak situations. This is mainly due to the need to induce flagellar growth for optimizing agglutination reactions for H antigens. In addition, since there are many serotypes of H antigens, multiple agglutination steps have to be performed. There are 53 H types of E. coli flagella in total (designated H1 to H56; H13, H22, and H50 no longer exist) (4, 5). They are composed of polymerized flagellin proteins, each with an average molecular mass of approximately 50 kDa (36 to 60 kDa).Since H antigens take longer to be typed with antisera, flagellar gene-based molecular methods, such as PCR-based flagellar gene sequen...

Purpose:The need for rapid and accurate H typing is evident during Escherichia coli outbreak situations. This study explores the transition of MS-H, a method originally developed for rapid H antigen typing of E. coli using LC-MS/MS of flagella digest of reference strains and some clinical strains, to E. coli isolates in clinical scenario through quantitative analysis and method validation. Experimental design: Motile and nonmotile strains were examined in batches to simulate clinical sample scenario. Various LC-MS/MS batch run procedures and MS-H typing rules were compared and summarized through quantitative analysis of MS-H data output for a standard method development. Results: Label-free quantitative data analysis of MS-H typing was proven very useful for examining the quality of MS-H result and the effects of some sample carryovers from motile E. coli isolates. Based on this, a refined procedure and protein identification rule specific for clinical MS-H typing was established and validated. Conclusions and clinical relevance: With LC-MS/MS batch run procedure and database search parameter unique for E. coli MS-H typing, the standard procedure maintained high accuracy and specificity in clinical situations, and its potential to be used in a clinical setting was clearly established.