Pulsed-field gel electrophoresis (PFGE): A review of the "gold standard" for bacteria typing and current alternatives

Genetic Profiles and Invasion Ability of Listeria monocytogenes Isolated from Bovine Carcasses in Southern Brazil

ABSTRACT

The goals of this study were to evaluate the persistence and the virulence potential of Listeria monocytogenes isolated from beef carcasses obtained in processing facilities in the southern region of Rio Grande do Sul, Brazil, based on pulsed-field gel electrophoresis (PFGE), invasion ability in human colorectal carcinoma cells (HCT-116), internalin A (InlA) expression by Western blot, and identification of mutation points in inlA. PFGE profiles demonstrated that L. monocytogenes isolates were grouped based on their previously identified lineages and serogroups (lineage I: serogroup IIb, n = 2, and serogroup IVb, n = 5; lineage II: serogroup IIc, n = 5). Isolates with indistinguishable genetic profiles through this method were obtained from different slaughterhouses and sampling steps, with as much as a 3-year interval. Seven isolates showed high invasion ability (2.4 to 7.4%; lineage I, n = 6, and lineage II, n = 1) in HCT and expressed InlA. Five isolates showed low cell invasion ability (0.6 to 1.4%; lineage I, n = 1, and lineage II, n = 4) and did not express InlA, and two of them (lineage II, serogroup IIc) presented mutations in inlA that led to premature stop codon type 19 at position 326 (GAA → TAA). The results demonstrated that most L. monocytogenes isolates from lineage I expressed InlA and were the most invasive in HCT, indicating their high virulence potential, whereas most isolates from lineage II showed attenuated invasion because of nonexpression of InlA or the presence of premature stop codon type 19 in inlA. The obtained results demonstrated that L. monocytogenes with indistinguishable PFGE profiles can persist or be reintroduced in beef processing facilities in the studied region and that differences in their virulence potential are based on their lineages and serogroups.

HIGHLIGHTS

Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening

IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of IRBT to detect probiotics has rarely been reported. Herein, we evaluated the discriminatory power of IRBT to type Lactiplantibacillus plantarum isolates at the strain level and explored its application potential in probiotic preliminary selection. Twenty Lactiplantibacillus isolates collected from pickled radishes during successive fermentation were used to test the robustness of IRBT at the strain level. IRBT was then compared with genotyping methods such as whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to evaluate its discrimination power. IRBT distributed the 20 isolates into five clusters, with L. argentoratensis isolate C7-83 being the most distant from the other isolates, which belonged to L. plantarum. IRBT showed good reproducibility, although deviation in the discriminative power of IRBT was found at the strain level across laboratories, probably due to technical variance. All examined methods allowed bacterial identification at the strain level, but IRBT had higher discriminatory power than MLST and was comparable to the WGS and PFGE. In the phenotypic comparison study, we observed that the clustering results of probiotic physiological attributes (e.g., sensitivity to acid and bile salts, hydrophobicity of the cell surface, and resistance to antibiotics) were consistent with the typing results of IRBT. Our results indicated that IRBT is a robust tool for L. plantarum strain typing that could improve the efficiency of probiotic identification and preliminary screening, and can potentially be applied in probiotic traceability and quality control.

Genomic Investigation Reveals a Community Typhoid Outbreak Caused by Contaminated Drinking Water in China, 2016

Typhoid fever is a life-threatening disease caused by Salmonella enterica serovar Typhi (S. Typhi) and remains a significant public health burden in developing countries. In China, typhoid fever is endemic with a limited number of reported outbreaks. Recently, Chinese local Center for Disease Prevention and Control is starting to apply whole genome sequencing for tracking the source of outbreak isolates. In this study, we conducted a retrospective investigation into a community outbreak of typhoid fever in Lanling, China, in 2016. A total of 26 S. Typhi isolates were recovered from the drinking water (n = 1) and patients' blood (n = 24) and stool (n = 1). Phylogenetic analysis indicated the persistence of the outbreak isolates in drinking water for more than 3 months. The genomic comparison demonstrated a high similarity between the isolate from water and isolates from patients in their genomic content, virulence gene profiles, and antimicrobial resistance gene profile, indicating the S. Typhi isolate from drinking water was responsible for the examined outbreak. The result of pulsed-field gel electrophoresis (PFGE) revealed these isolates had identical PFGE pattern, indicating they are clonal variants. Additionally, phylogeographical analysis of global S. Typhi isolates suggested the outbreak isolates are evolutionarily linked to the isolates from the United Kingdom and Vietnam. Taken together, this study highlights the drinking water and international travel as critical control points of mitigating the outbreak, emphasizing the necessity of regular monitoring of this pathogen in China.

Legionella pneumophila in Municipal Shower Systems in Stavanger, Norway; A Longitudinal Surveillance Study Using Whole Genome Sequencing in Risk Management

Following an incidence of Legionnaires disease (LD) in 2007, where a municipal shower system was the likely source of infection, Stavanger municipality initiated a surveillance program for Legionella as part of establishing internal risk evaluation and prevention routines. More than 250 shower systems were examined for cultivatable Legionella pneumophila. The prevalence and diversity of serogroups (sg) and sequence types (STs) of L. pneumophila were mapped using available typing techniques over a period of more than 10 years (2010–2021). The surveillance showed an overall reduction in the L. pneumophila colonisation rate in municipal systems from 11 to 4.5% following prevention measures during the period, with the highest colonisation rate in complex systems (e.g., larger nursing homes and sports complexes). Further, an approximately even distribution between sg1 and 2–14 was seen. Whole genome sequencing (WGS) revealed that only a limited number of STs were detected, and they were consistent at specific locations over time. This study showed that environmental surveillance data in combination with available typing techniques and WGS can give the municipality a better tool for risk management and an overview of ST distributions that can be a valuable asset in future source investigations.

Phenotypic and Genotypic Characterization of Salmonella Isolates Recovered from Foods Linked to Human Salmonellosis Outbreaks in Minas Gerais State, Brazil

ABSTRACT

Salmonella is one of the primary pathogens that causes foodborne diseases worldwide. In the present study, we characterized Salmonella isolates recovered from foods linked to human salmonellosis outbreaks in Minas Gerais, Brazil, from 2003 to 2017. Serotype, antimicrobial susceptibility, presence of virulence genes, and genetic polymorphism as determined by repetitive element sequence-based PCR were determined for 70 Salmonella isolates. Thirteen Salmonella serotypes were identified, and the most prevalent were Enteritidis and Typhimurium, comprising 52 (74.3%) of the 70 isolates. Sixty-five (92.8%) of the isolates were resistant to at least 1 of the 15 antimicrobials tested. Ten isolates (14.2%) had a multidrug resistance phenotype. Isolates were screened for 16 virulence genes, which were found in 75.7 to 100% of the isolates. A statistical difference was found among Salmonella serotypes in the presence of the sipB, sopE, lfpA, sefA, and spvC genes. Based on their DNA fingerprints, 40 isolates of Salmonella Enteritidis from 16 outbreaks were separated into 14 groups and 12 isolates of Salmonella Typhimurium were separated into 6 groups. These serological patterns were similar to those reported by public health centers worldwide. Of concern is the high prevalence among the isolates in this study of both virulence genes and resistance to antimicrobials, especially to critically important drugs. Special attention should be given to Salmonella Enteritidis. Although the genomes of these Salmonella isolates were relatively variable, high genetic similarity was observed among them, and some had identical fingerprints. These results support the hypothesis of clonal circulation of Salmonella isolates causing human infections in Minas Gerais.

HIGHLIGHTS

A Severe Gastroenteritis Outbreak of Salmonella enterica Serovar Enteritidis Linked to Contaminated Egg Fried Rice, China, 2021

Salmonella contamination of eggs and egg shells has been identified as a public health problem worldwide. Here, we reported an outbreak of severe gastrointestinal symptoms caused by Salmonella enterica serovar Enteritidis (S. enteritidis) in China. We evaluated the outbreak by using epidemiological surveys, routine laboratory testing methods, and whole genome sequencing (WGS). This outbreak occurred in a canteen in Beijing, during March 9–11, 2021, 225 of the 324 diners who have eaten at the canteen showed gastrointestinal symptoms. The outbreak had characteristical epidemiological and clinical features. It caused a very high attack rate (69.4%) in a short incubation time. All patients developed diarrhea and high fever, accompanied by abdominal pain (62.3%), nausea (50.4%), and vomiting (62.7%). The average frequency of diarrhea was 12.4 times/day, and the highest frequency of diarrhea was as high as 50 times/day. The average fever temperature was 39.4°C, and the highest fever temperature was 42°C. Twenty strains of S. enteritidis were recovered, including 19 from the patients samples, and one from remained egg fried rice. Antibiotic susceptibility test showed that the 20 outbreak strains all had the same resistance pattern. PFGE results demonstrated that all 20 strains bore completely identical bands. Phylogenetic analysis based on WGS revealed that all 20 outbreak strains were tightly clustered together. So the pathogenic source of this food poisoning incident may was contaminated egg fried rice. Resistance gene analysis showed that the outbreak strains are all multi-drug resistant strains. Virulence gene analysis indicated that these outbreak strains carried a large number of virulence genes, including 2 types of Salmonella pathogenicity islands (SPI-1 and SPI-2). Other important virulence genes were also carried by the outbreak strains, such as pefABCD, rck and shdA. And the shdA gene was not in other strains located in the same evolutionary branch as the outbreak strain. We speculated that this is a significant reason for the serious symptoms of gastroenteritis in this outbreak. This outbreak caused by S. enteritidis suggested government should strengthen monitoring of the prevalence of outbreak clone strains, and take measures to mitigate the public health threat posed by contaminated eggs.

Acidogenic and aciduric properties of Streptococcus mutans serotype c according to its genomic variability

Streptococcus mutans (S. mutans) has a wide genetic diversity that contributes to its phenotypic heterogeneity, and may be related to attributes associated with acidogenicity and aciduricity. The aim of this study was to evaluate the acidogenic and aciduric properties of S. mutans serotype c isolates from saliva of schoolchildren according to the genomic variability. S. mutans isolates were identified by polymerase chain reaction. Fifty S. mutans serotype c isolates were genotyped by pulsed field gel electrophoresis and tested for their ability to produce and resist acid. Three specific genotypes were identified in the caries-active group and only one in the caries-free group. Although isolates were similarly acidogenic, an exclusive caries-active genotype had the greatest glycolytic activity. In contrast, isolates exhibited variable aciduricity, and three caries-active genotypes were the least aciduric. We concluded that there is genetic variability within serotype c. Acid production was similar regardless of the caries status but correlated with the number of genotypes. In addition, resistance to acid could be an important characteristic for the establishment and colonisation of specific genotypes in children with caries. However, it is important to evaluate children's intrinsic characteristics and other phenotypic properties to explain the physiopathological behaviour of the different genotypes.

Detection of synergistic antimicrobial resistance mechanisms in clinical isolates of Pseudomonas aeruginosa from post-operative wound infections

Infections caused by carbapenem-resistant Pseudomonas aeruginosa are life-threatening due to its synergistic resistance mechanisms resulting in the ineffectiveness of the used antimicrobials. This study aimed to characterize P. aeruginosa isolates for antimicrobial susceptibility, biofilm formation virulence genes, and molecular mechanisms responsible for resistance against various antimicrobials. Out of 700 samples, 91 isolates were confirmed as P. aeruginosa which were further classified into 19 non-multidrug-resistant (non-MDR), 7 multidrug-resistant (MDR), 19 extensively drug-resistant (XDR), and 8 pan drug-resistant (PDR) pulsotypes based on standard Kirby Bauer disc diffusion test and pulse field gel electrophoresis. In M9 minimal media, strong biofilms were formed by the XDR and PDR pulsotypes as compared to the non-MDR pulsotypes. The virulence genes, responsible for the worsening of wounds including LasB, plcH, toxA, and exoU, were detected among all MDR, XDR, and PDR pulsotypes. Carbapenemase activity was phenotypically detected in 45% pulsotypes and the responsible genes were found as bla_GES (100%), bla_VIM (58%), bla_IMP (4%), and bla_NDM (4%). Real-time polymerase chain reaction showed the concomitant use of multiple mechanisms such as oprD under-expression, enhanced efflux pump activity, and ampC overexpression in the resistant isolates. Polymyxin is found as the only class left with more than 80% susceptibility among the isolates which is an alarming situation suggesting appropriate measures to be taken including alternative therapies. KEY POINTS: • Multidrug-resistant P. aeruginosa isolates formed stronger biofilms in minimal media. • Only polymyxin antimicrobial was found effective against MDR P. aeruginosa isolates. • Under-expression of oprD and overexpression of ampC were found in resistant isolates.

Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii Isolated from the Intensive Care Unit in a Tertiary Teaching Hospital in Malaysia

The emergence of carbapenem-resistant Acinetobacter baumannii (CRAB) has now become a global sentinel event. CRAB infections often instigate severe clinical complications and are potentially fatal, especially for debilitated patients. The present study aimed to conduct molecular characterization on CRAB isolated from patients in the intensive care unit from 2015 to 2016 and determine the risk factors associated with patients’ mortality. One hundred CRAB isolates were retrospectively selected and included in this study. Antimicrobial susceptibility testing showed that all isolates remained susceptible to colistin, even though 62% of them conferred resistance to all other classes of antibiotics tested. OXA carbapenemase gene was found to be the predominant carbapenemase gene, with 99% of the isolates coharbouring bla_OXA-23-like and bla_OXA-51-like carbapenemase genes. All isolates were carrying intact CarO genes, with the presence of various degree of nucleotide insertion, deletion and substitution. Overall, PFGE subtyped the isolates into 13 distinct pulsotypes, with the presence of 2 predominant pulsotypes. Univariate analysis implied that age, infection/colonization by CRAB, ethnicity, comorbidity and CRAB specimen source were significantly associated with in-hospital mortality. Multivariate analysis identified a higher risk of mortality for patients who are of Chinese ethnicity with diabetes as an underlying disease. As CRAB infection could lead to high rate of mortality, comprehensive infection control measures are needed to minimize the spread of this pathogen.

ON-rep-seq as a rapid and cost-effective alternative to whole-genome sequencing for species-level identification and strain-level discrimination of Listeria monocytogenes contamination in a salmon processing plant

Identification, source tracking, and surveillance of food pathogens are crucial factors for the food-producing industry. Over the last decade, the techniques used for this have moved from conventional enrichment methods, through species-specific detection by PCR to sequencing-based methods, whole-genome sequencing (WGS) being the ultimate method. However, using WGS requires the right infrastructure, high computational power, and bioinformatics expertise. Therefore, there is a need for faster, more cost-effective, and more user-friendly methods. A newly developed method, ON-rep-seq, combines the classical rep-PCR method with nanopore sequencing, resulting in a highly discriminating set of sequences that can be used for species identification and also strain discrimination. This study is essentially a real industry case from a salmon processing plant. Twenty Listeria monocytogenes isolates were analyzed both by ON-rep-seq and WGS to identify and differentiate putative L. monocytogenes from a routine sampling of processing equipment and products, and finally, compare the strain-level discriminatory power of ON-rep-seq to different analyzing levels delivered from the WGS data. The analyses revealed that among the isolates tested there were three different strains. The isolates of the most frequently detected strain (n = 15) were all detected in the problematic area in the processing plant. The strain level discrimination done by ON-rep-seq was in full accordance with the interpretation of WGS data. Our findings also demonstrate that ON-rep-seq may serve as a primary screening method alternative to WGS for identification and strain-level differentiation for surveillance of potential pathogens in a food-producing environment.

Genotype and virulence gene analyses of Bacillus cereus group clinical isolates from the Chinese softshell turtle (Pelodiscus sinensis) in Taiwan

Chinese softshell turtles (Pelodiscus sinensis) (CST) are susceptible to infections by bacteria belonging to the Bacillus cereus group (Bcg). Bcg includes several closely related species, two of which, B. cereus and B. thuringiensis, are pathogens of aquatic animals or insects. In the present study, we collected 57 Bcg isolates obtained from diseased CST from 2016 to 2019 in Kaohsiung and Pingtung, the areas with the most CST farms in Taiwan. All isolates were divided into four genotypes with two restriction enzymes, SmaI and NotI, by pulsed-field gel electrophoresis and enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). Representative isolates from each genotype were subjected to phylogenetic tree analysis using 16S rDNA and pyruvate carboxylase genes as phylogenetic markers, and these CST isolates appeared in different clades. PCR was performed targeting six selected virulence genes, four of which were detected in CST isolates, including cytotoxin K (1/57), hblC of the haemolysin BL complex (46/57), nheA of the non-haemolytic enterotoxin complex (52/57) and enterotoxin FM (57/57), whereas cereulide synthetase and cereulide peptide synthase-like genes were not detected in any isolates.

Bifidobacteria Strain Typing by Fourier Transform Infrared Spectroscopy

Fourier transform infrared (FTIR) spectroscopy, a technology traditionally used in chemistry to determine the molecular composition of a wide range of sample types, has gained growing interest in microbial typing. It is based on the different vibrational modes of the covalent bonds between atoms of a given sample, as bacterial cells, induced by the absorption of infrared radiation. This technique has been largely used for the study of pathogenic species, especially in the clinical field, and has been proposed also for the typing at different subspecies levels. The high throughput, speed, low cost, and simplicity make FTIR spectroscopy an attractive technique also for industrial applications, in particular, for probiotics. The aim of this study was to compare FTIR spectroscopy with established genotyping methods, pulsed-field gel electrophoresis (PFGE), whole-genome sequencing (WGS), and multilocus sequence typing (MLST), in order to highlight the FTIR spectroscopy potential discriminatory power at strain level. Our study focused on bifidobacteria, an important group of intestinal commensals generally recognized as probiotics. For their properties in promoting and maintaining health, bifidobacteria are largely marketed by the pharmaceutical, food, and dairy industries. Strains belonging to Bifidobacterium longum subsp. longum and Bifidobacterium animalis subsp. lactis were taken into consideration together with some additional type strains. For B. longum subsp. longum, it was possible to discriminate the strains with all the methods used. Although two isolates were shown to be strictly phylogenetically related, constituting a unique cluster, based on PFGE, WGS, and MLST, no clustering was observed with FTIR. For B. animalis subsp. lactis group, PFGE, WGS, and MLST were non-discriminatory, and only one strain was easily distinguished. On the other hand, FTIR discriminated all the isolates one by one, and no clustering was observed. According to these results, FTIR analysis is not only equivalent to PFGE, WGS, and MLST, but also for some strains, in particular, for B. animalis subsp. lactis group, more informative, being able to differentiate strains not discernible with the other two methods based on phenotypic variations likely deriving from certain genetic changes. Fourier transform infrared spectroscopy has highlighted the possibility of using the cell surface as a kind of barcode making tracing strains possible, representing an important aspect in probiotic applications. Furthermore, this work constitutes the first investigation on bifidobacterial strain typing using FTIR spectroscopy.

Comparison of Conventional Molecular and Whole-Genome Sequencing Methods for Differentiating Salmonella enterica Serovar Schwarzengrund Isolates Obtained from Food and Animal Sources

Over the last decade, Salmonella enterica serovar Schwarzengrund has become more prevalent in Asia, Europe, and the US with the simultaneous emergence of multidrug-resistant isolates. As these pathogens are responsible for many sporadic illnesses and chronic complications, as well as outbreaks over many countries, improved surveillance is urgently needed. For 20 years, pulsed-field gel electrophoresis (PFGE) has been the gold standard for determining bacterial relatedness by targeting genome-wide restriction enzyme polymorphisms. Despite its utility, recent studies have reported that PFGE results correlate poorly with that of closely related outbreak strains and clonally dominant endemic strains. Due to these concerns, alternative amplification-based molecular methods for bacterial strain typing have been developed, including clustered regular interspaced short palindromic repeats (CRISPR) and multilocus sequence typing (MLST). Furthermore, as the cost of sequencing continues to decrease, whole genome sequencing (WGS) is poised to replace other molecular strain typing methods. In this study, we assessed the discriminatory power of PFGE, CRISPR, MLST, and WGS methods to differentiate between 23 epidemiologically unrelated S. enterica serovar Schwarzengrund isolates collected over an 18-year period from distinct locations in Taiwan. The discriminatory index (DI) of each method for different isolates was calculated, resulting in values between 0 (not discriminatory) and 1 (highly discriminatory). Our results showed that WGS has the greatest resolution (DI = 0.982) compared to PFGE (DI = 0.938), CRISPR (DI = 0.906), and MLST (DI = 0.463) methods. In conclusion, the WGS typing approach was shown to be the most sensitive for S. enterica serovar Schwarzengrund fingerprinting.

Behind Every Great Infection Prevention Program is a Great Microbiology Laboratory: Key Components and Strategies for an Effective Partnership

A great clinical microbiology laboratory supporting a great infection prevention program requires focusing on the following services: rapid and accurate identification of pathogens associated with health care-associated infections; asymptomatic surveillance for health care-acquired pathogens before infections arise; routine use of broad and flexible antimicrobial susceptibility testing to direct optimal therapy; implementation of epidemiologic tracking tools to identify outbreaks; development of clear result communication with interpretative comments for clinicians. These goals are best realized in a collaborative relationship with the infection prevention program so that both can benefit from the shared priorities of providing the best patient care.

Prevalence and molecular characterization of Listeria monocytogenes isolated from wastewater of cattle slaughterhouses in Turkey

AIM

The study aimed to investigate the role of cattle slaughterhouse wastewater as a possible source for the environmental distribution of Listeria monocytogenes.

METHODS AND RESULTS

Listeria spp. isolation was performed by collecting 117 wastewater samples from four different cattle slaughterhouses in Turkey. Species-specific identification was performed biochemically, and L. monocytogenes isolates were confirmed with polymerase chain reaction (PCR). In all, 71 (62.2%) of the wastewater samples were found to be positive for Listeria spp., and 17 (14.9%) of these samples were contaminated with L. monocytogenes. Pulsed field gel electrophoresis (PFGE) analysis revealed that all L. monocytogenes isolates were of different pulsotypes and isolates belonged to seven different phylogenetic clusters. Multiplex PCR analysis for genoserotypes and lineage determination showed that the isolates were divided into genoserotypes IVb and IIc in Lineages I and II. Also, it has been investigated with SYBR-Green Real-time PCR whether the L. monocytogenes isolates harboured virulence genes (hly, sigB, plcA, plcB, inlA, inlB, inlC and inlJ), and it was found that all isolates were substantially positive. Antibiotic resistance profiles and MIC values of the isolates were determined, and all L. monocytogenes isolates were found susceptible to ampicillin. In contrast, two isolates were resistant to meropenem and erythromycin, and three isolates were resistant to trimethoprim/sulfamethoxazole.

CONCLUSION

L. monocytogenes, which pose a threat to public health and resists to antibiotics effectively used in treatments, can environmentally spread via wastewater of cattle slaughterhouses. The wastewater of the food industry, which has rich microbiota, should be treated carefully, and possible environmental contamination should be prevented.

SIGNIFICANCE AND IMPACT OF STUDY

This is the first study that investigates the molecular characterization of L. monocytogenes isolated from cattle slaughterhouse wastewater and the findings represent the importance of cattle wastewater in the epidemiology of L. monocytogenes in Turkey.

Analysis of the molecular characteristics of a blaKPC-2-harbouring untypeable plasmid in Serratia marcescens

INTRODUCTION

Serratia marcescens has attracted increasing attention worldwide as a neglected opportunistic pathogen of public health concern, especially due to its antimicrobial resistance features, which usually cause nosocomial infections in immunocompromised or critically ill patients.

METHODS

In our study, four carbapenem-resistant Serratia marcescens (CRSM) clinical isolates were characterized in our hospital from February 2018 to May 2018. The conjugation experiment confirmed the transferability of the carbapenem resistance gene. The types of carbapenem resistance genes were detected by PCR. The homology of the strains was analysed by pulsed field gel electrophoresis (PFGE). The characteristics of the plasmid and environment of carbapenem resistance genes were analysed after whole genome sequencing was performed. Then, we compared the amino acid sequence of the replication initiation protein and constructed a dendrogram by the neighbour-joining method.

RESULTS

All four isolates showed carbapenem resistance conferred by a blaKPC-2-harbouring plasmid. They had exactly the same bands confirmed by PFGE and were defined as the homologous strains. The blaKPC-2 genes in all of the isolates were located in a 42,742 bp plasmid, which was located in the core region of antibiotic resistance and was composed of Tn3 family transposons, recombinant enzyme genes, ISKpn6 and ISKpn27. The core region of antibiotic resistance formed a 'Tn3-ISKpn6-blaKPC-ISKpn27-Tn3' structure, which was an independent region as a movable element belonging to transposon Tn6296 and its derivatives. The plasmid had a similar skeleton to incX6 plasmids and a similar amino acid sequence to the replication initiation protein. The plasmid was defined as an untypeable blaKPC-2-harbouring plasmid named the 'IncX6-like' plasmid.

CONCLUSION

The four CRSM isolates were mainly clonally disseminated with a blaKPC-2-harbouring plasmid in our hospital. The pKPC-2-HENAN1602 plasmid (CP047392) in our study was first reported in Serratia marcescens, which belongs to an untypeable group named the 'IncX6-like' plasmid. The carbapenem-resistant gene structure surrounding blaKPC-2 as a sole accessory module can be acquired by horizontal gene transfer and might lead to serious nosocomial infection.

Evaluation of the IR Biotyper for Klebsiella pneumoniae typing and its potentials in hospital hygiene management

Klebsiella pneumoniae has emerged as one of the most important pathogens that frequently encounter in community-acquired or hospital-acquired infections. Timely epidemiological surveillance could greatly facilitate infection control of K. pneumoniae and many deadly pathogens alike. In this study, we evaluated the performance of the IR Biotyper, a Fourier transform infrared (FTIR) spectroscopy system for K. pneumoniae isolates typing through (i) optimizing the culture scheme and defining the cutoff value (COV) range and (ii) comparing with commonly used typing tools such as multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS). We found that a non-selective and non-chromogenic medium with 24 ± 2 h incubation gives the best discriminatory power for the IR Biotyper (IRBT). COV evaluation indicated that the IRBT is a robust typing method with good reproducibility. Besides, we observed that the modified H2 O-EtOH suspensions preparation method could enhance the quality of the spectrum, especially for those hypermucoviscous strains. For the method comparison study, our data demonstrated that FTIR spectroscopy could accurately cluster K. pneumoniae strains. The typing results of the IRBT were almost entirely in concordance with those from PFGE and WGS. Together with the advantages such as low costs and short turnaround time (less than 3h), the IRBT is a promising tool for strain typing that could make real-time outbreak investigation a reality.

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

Multilocus variable-number tandem-repeat analysis (MLVA) is a widely accepted molecular typing tool for enterohemorrhagic Escherichia coli (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. On performing MLVA against 51 EHEC O157 isolates, the repeat numbers of 46 isolates were determined accurately using the look-up table with a 99% prediction interval, an outcome superior to that when using a 95% prediction interval. For the remaining five isolates, although the electrophoresis size fell outside the look-up table, we were able to predict the repeat number accurately by extrapolation or the nearest values of the look-up table. Our approach provides more accurate results than a nonadjusted conventional look-up table for calibrating MLVA profiles.

Unusual finding of the human-adapted hypervirulent serotype III/ST17 clone in a historical bovine Group B Streptococcus isolate from Brazil

Group B Streptococcus (GBS) is a leading cause of human neonatal infections and bovine mastitis. We report here the unusual finding of the human-adapted hypervirulent serotype III/ST17 clone in a bovine GBS isolated in 1987 in Brazil. This isolate shared several phenotypic and genotypic characteristics with serotype III/ST17 strains obtained from human sources, including PFGE pattern, pilus genes, lactose fermentation, DNase activity, and antimicrobial susceptibility profile, highlighting the importance of continued tracking of GBS in the One Health scope. The study brings new evidence for the potential interspecies transmission and sheds new light into evolution aspects of the pathogen Group B Streptococcus (GBS) by reporting the occurrence of an ancient bovine GBS isolate belonging to a variant currently known to be exclusively found in human hosts.

Antimicrobial resistance and genotyping of Staphylococcus aureus obtained from food animals in Sichuan Province, China

Background

Staphylococcus aureus (S. aureus), especially methicillin-resistant Staphylococcus aureus (MRSA), is considered a common zoonotic pathogen, causing severe infections. The objective of this study was to investigate the antimicrobial susceptibility, resistance genes and molecular epidemiology among MRSA and methicillin-susceptible Staphylococcus aureus (MSSA) isolated from food animals in Sichuan Province, China.

Methods

This study was conducted on 236 S. aureus isolates. All isolates were subjected to antimicrobial susceptibility testing by using a standard microbroth dilution method. The Polymerase Chain Reaction (PCR) was performed to identify genes encoding the β-lactams resistance (blaZ, mecA), macrolides (ermA, ermB, ermC) and aminoglycosides (aacA-aphD). The molecular structures and genomic relatedness of MRSA isolates were determined by staphylococcal chromosome cassette mec (SCCmec) typing and pulsed-field gel electrophoresis (PFGE), respectively.

Results

Among 236 isolates, 24 (10.17 %) were recognized as MRSA. MRSA isolates showed different resistance rates to 11 antimicrobials ranging from 33.33 to 100 %, while for MSSA isolates the rates varied from 8.02 to 91.51 %. Multi-drug resistance phenotype was found in all MRSA isolates. The ermC gene encoding macrolides-lincosamides-streptogramin B was the most prevalent gene detected in 87.29 % of the S. aureus isolates, followed by ermB (83.05 %), blaZ (63.98 %), aacA-aphD (44.07 %), ermA (11.44 %) and mecA (11.02 %) genes. The prevalence of resistance genes in MRSA isolates was significantly higher than that of MSSA. Regarding the molecular morphology, SCCmec III (12/24, 50 %) was the most common SCCmec type. Furthermore, the PFGE typing showed that 24 MRSA were divided into 15 cluster groups (A to O), the major pulsotype J encompassed 25 % of MRSA isolates.

Conclusions

The S. aureus isolates from food animals in Sichuan province of China have severe antimicrobials resistance with various resistance genes, especially MRSA isolates. Additionally, the genetic pool of MRSA isolates is diverse and complex, and further investigation is necessary.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12917-021-02884-z.

Subtyping β-lactamase-producing Escherichia coli strains isolated from patients with UTI by MLVA and PFGE methods

OBJECTIVES

Strain subtyping is an important epidemiological tool to trace contamination, determine clonal relationships between different strains, and the cause of outbreaks. Current subtyping methods, however, yield less than optimal subtype discrimination. Pulsed-field gel electrophoresis is the gold standard method for Escherichia coli and Multiple-Locus Variable-number tandem repeat Analysis is a rapid PCR-based method. The purpose of this study was to evaluate MLVA and PFGE methods for subtyping β -lactamase-producing E. coli strains isolated from urinary tract infections.

MATERIALS AND METHODS

Overall, 230 E. coli isolates from patients with urinary tract infections were examined for antimicrobial susceptibility testing. 10-loci and 7-loci MLVA and PFGE methods were used for molecular typing of β -lactamase-producing E. coli isolates.

RESULTS

Out of 230 isolates, 130 (56.5%) β -lactamase-producing E. coli isolates were found in this study. The diversity indices of the VNTR loci showed an average diversity of 0.48 and 0.54 for 7-loci and 10-loci MLVA, respectively. The discriminatory power of PFGE showed a value of 0.87. The discordance between the methods was high.

CONCLUSION

Our study showed that PFGE is more discriminatory than MVLA. MLVA is a PCR- based method and can generate unmistakable data, in contrast to PFGE. Optimization of polymorphic VNTR is essential to improve the discriminatory power of MLVA based on geographical region.

Molecular Typing of Salmonella by Pulsed-Field Gel Electrophoresis

Salmonella is recognized as a major human foodborne pathogen and threat to public health world widely. It is important to carry out epidemiological investigations to determine the primary sources of bacterial contamination. Pulsed-field gel electrophoresis (PFGE) is an important method of the molecular typing, and play an important role in tracking the sources of infection and epidemic control. The PFGE is currently considered as "gold standard" of molecular typing methods for bacterial foodborne pathogen. Here, we describe the PFGE protocol to type the Salmonella from pork.

Molecular Characterization of Carbapenem Resistant Klebsiella pneumoniae in Malaysia Hospital

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) is a great concern, as carbapenems are the last-line therapy for multidrug-resistant Gram-negative bacteria infections. This study aims to report the epidemiology of CRKP in a teaching hospital in Malaysia based on the molecular genotypic and clinical characteristics of the isolates. Sixty-three CRKP strains were isolated from a tertiary teaching hospital from January 2016 until August 2017. Carbapenemase genes were detected in 55 isolates, with bla_OXA-48 (63.5%) as the predominant carbapenemase gene, followed by bla_NDM (36.5%). At least one porin loss was detected in nine isolates. Overall, 63 isolates were divided into 30 clusters at similarity of 80% with PFGE analysis. Statistical analysis showed that in-hospital mortality was significantly associated with the usage of central venous catheter, infection or colonization by CRKP, particularly NDM-producers. In comparison, survival analysis using Cox proportional hazards regression identified a higher hazard ratio for patients with a stoma and patients treated with imipenem but a lower hazard ratio for patients with NDM-producing CRKP. OXA-48 carbapenemase gene was the predominant carbapenemase gene in this study. As CRKP infection could lead to a high rate of in-hospital mortality, early detection of the isolates was important to reduce their dissemination.

A Case-Control Study on the Association between Salmonella Bacteriuria and Cystoscopy

To date, there is only one published report of an outbreak of urinary tract infections by Salmonella species after cystoscopy. Disinfection procedures for cystoscope have come into question. The current study aimed to determine the odds of developing Salmonella bacteriuria after cystoscopy. A retrospective case-control study was conducted on all patients with Salmonella species in urine (case) and blood (control) from 2017 to 2019 in 16 hospitals in Eastern Ontario, Canada. Eight of the 11 patients had cystoscopy prior to Salmonella bacteriuria; three of the 74 patients had urological procedures prior to Salmonella bacteremia, but none of their procedures were cystoscopy. The odds ratio of urological procedures with Salmonella bacteriuria was 63.1 (95% CI 10.9 to 366.6; p < 0.0001). In the bacteriuria group, the most frequently identified isolates were Salmonella enteritidis (n = 8), followed by Salmonella oranienburg, and Salmonella heidelberg. Seven of the S. enteritidis isolates had identical susceptibilities (ampicillin-sensitive; sulfamethoxazole/trimethoprim-sensitive; ciprofloxacin intermediate). In the bacteremia group, the most frequently identified isolates were S. enteritidis (n = 22), followed by Salmonella typhi, S. heidelberg, S. oranienburg, and Salmonella typhimurium. The result suggested cystoscopy is a risk factor for Salmonella bacteriuria. Identification of Salmonella bacteriuria should prompt public health investigations of linkage between cystoscopy and Salmonella bacteriuria.

Prevalence and antimicrobial resistance of Listeria species and molecular characterization of Listeria monocytogenes isolated from retail ready-to-eat foods

A wide variety of foods can be contaminated with Listeria species, especially L. monocytogenes. Ready-to-eat (RTE) foods are predominantly associated with human listeriosis caused by L. monocytogenes. Therefore, this study aimed to assess the presence of Listeria species in RTE foods and to characterize L. monocytogenes isolates by means of detection of virulence markers, serotypes and genetic relatedness. Of the 300 RTE food samples, 59 (19.7%) were positive for Listeria species: L. innocua (13.3%), L. monocytogenes (5%), L. welshimerii (2.3%), L. grayi subsp. murrayi (1.3%), L. grayi (1%), L. ivanovii (1%) and L. ivanovi subsp. londoniensis (0.3%). All L. monocytogenes isolates identified were positive for the actA, iap, inlA, inlB, inlC, inlJ, plcA and prfA virulence genes and biofilm. The isolates were serotyped as 1/2c (33.3%), 4b (26.7%), 1/2a (26.7%), 1/2b (6.7%) and 3c (6.7%) by the multiplex-PCR and agglutination methods. PCR-restriction fragment length polymorphism with AluI and MluCI resulted in three and two profiles, respectively. Pulsed-field gel electrophoresis differentiated the L. monocytogenes isolates into 15 ApaI and 12 AscI patterns. Antimicrobial resistance of all Listeria isolates was determined by the disk diffusion method. Most L. monocytogenes isolates were sensitive to antimicrobials used in the treatment of listeriosis. This study shows the presence of potential pathogenic and antimicrobial-resistant L. monocytogenes in RTE foods that may lead to consumer health risks.

Streptococcus dysgalactiae-Contagious or Environmental?

Simple Summary

The usual routes of transmission of Streptococcus dysgalactiae in the development of bovine mastitis are unclear. For the control of mastitis in dairy practice, improved knowledge about the transmission of this pathogen would be very helpful. The variety of strain within a herd can be used to describe its transmission behavior. Isolates of Strep. dysgalactiae were collected from clinical mastitis samples on different farms, and the strains were typed using a molecular method. Overall, we performed strain typing on isolates from 16 farms in Germany and found signs of the contagious transmission of Strep. dysgalactiae on all the farms. We observed a variety of outcomes, from a single strain in all six Strep. dysgalactiae cases recorded on one farm, to five strains in six cases recorded on another farm.

Abstract

Streptococcus dysgalactiae is among the most important pathogens causing bovine mastitis. Unfortunately, there is presently a lack of clear knowledge about the mode of transmission—contagious or environmental—of this pathogen. To obtain more information on this, knowledge of the genetic diversity of the isolated microorganisms at the farm level can be useful. To observe the strain variety in different herds of cattle, isolates of Strep. dysgalactiae were collected from clinical mastitis samples at different farms, and the strains were typed using the pulsed-field gel electrophoresis (PFGE) method. Overall, we performed strain typing on 93 isolates from 16 farms in Germany and used an index to describe the degree of contagiosity of Strep. dysgalactiae at each farm. This index (CI) represents the number of isolates divided by the number of strains found in mastitis milk of clinical cases within a period of 14 months. The results differed between the farms. In one farm, all six Strep. dysgalactiae cases that occurred during the study period were caused by a single strain (CI = 6), while in another farm the six cases that occurred were caused by five different strains (CI = 1.2). All other farms fell between these two extremes. This indicates that Strep. dysgalactiae infections can occur via several routes of transmission. At the farm level, strain comparisons are necessary to determine the routes of transmission. Two strains were able to survive on the farm for a minimum of 14 months.

openPFGE: An open source and low cost pulsed-field gel electrophoresis equipment

DNA electrophoresis is a fundamental technique in molecular biology that allows the separation of DNA molecules up to ~50 Kbp. Pulsed-field gel electrophoresis [PFGE] is a variation of the conventional DNA electrophoresis technique that allows the separation of very large DNA molecules up to ~10 Mbp. PFGE equipment is very expensive and it becomes an access barrier to many laboratories. Also, just a few privative designs of the equipment are available and it becomes difficult for the community to improve or customize their functioning. Here, we provide an open source PFGE equipment capable of the separation of DNA molecules up to, at least, ~2 Mbp and at low cost: USD$850, about 3% of the price of typical commercial equipment.

Molecular typing tools for identifying and characterizing lactic acid bacteria: a review

Identification and classification of beneficial microbes is of the highest significance in food science and related industries. Conventional phenotypic approaches pose many challenges, and they may misidentify a target, limiting their use. Genotyping tools show comparatively better prospects, and they are widely used for distinguishing microorganisms. The techniques already employed in genotyping of lactic acid bacteria (LAB) are slightly different from one another, and each tool has its own advantages and disadvantages. This review paper compiles the comprehensive details of several fingerprinting tools that have been used for identifying and characterizing LAB at the species, sub-species, and strain levels. Notably, most of these approaches are based on restriction digestion, amplification using polymerase chain reaction, and sequencing. Nowadays, DNA sequencing technologies have made considerable progress in terms of cost, throughput, and methodology. A research journey to develop improved versions of generally applicable and economically viable tools for fingerprinting analysis is ongoing globally.

Molecular surveillance of methicillin-susceptible Staphylococcus aureus (MSSA) isolated over a one-year period from a Malaysian Teaching Hospital

Introduction

We report the results of a molecular surveillance study carried out on methicillin-susceptible Staphylococcus aureus (MSSA) isolated in a one-year duration from Hospital Canselor Tuanku Muhriz (HCTM), a tertiary hospital located in Kuala Lumpur, Malaysia.

Methods

The first strain isolated from each MSSA infection in HCTM during the year 2009 was included into the study. Antimicrobial susceptibility testing and agr group typing were carried out for all strains; virulence gene (cna, seh, TSST-1 and PVL) typing results of the strains were obtained from a previous study. Pulsed-field gel electrophoresis (PFGE) was done on selected strains from the orthopedic ward. Relationship(s) between different typing methods used in the study was investigated, where a p value of <0.05 indicated significant association between typing methods.

Results

A total of 880 MSSA strains were included into the study. The strains were generally susceptible to most antibiotics, with most of them carrying cna and agr-I (51.6%, n=454; 39.8%, n=350, respectively). A total of 17 PFGE pulsotypes were identified using an 80% similarity cut-off value, where the main pulsotype (pulsotype E) consisted of 24 isolates (23.5%). agr-III strains were found to be usually positive for both cna and seh (p<0.05). In addition, some PFGE pulsotypes were also characteristic of certain virulence genes or agr groups.

Conclusions

We did not identify a dominant MSSA clone circulating in HCTM in 2009. Nevertheless, results from this molecular surveillance will provide good baseline data for the hospital's second S. aureus surveillance planned for the year 2020.

Investigation of a healthcare-associated Candida tropicalis candidiasis cluster in a haematology unit and a systematic review of nosocomial outbreaks

BACKGROUND

Non-albicans Candida spp. are an emerging cause of hospital-acquired bloodstream infections, associated with high mortality due to the challenges in diagnosis and delayed treatment.

OBJECTIVES

We aimed to investigate a cluster of healthcare-associated invasive candidiasis caused by C tropicalis and review the literature of healthcare-associated outbreaks or clusters caused by C tropicalis.

METHODS

An investigation was performed to determine clinical presentation, treatment outcomes and the factors contributing to C tropicalis candidemia occurrence. We searched the Medline database via PubMed and Ovid using the keywords of "Candida tropicalis" combined with "outbreak" or "clustering" or "clusters," and we limited the search to studies conducted from January 1989 to January 2019.

RESULTS

We report two related cases of C tropicalis candidemia among patients with AML following a period of neutropenia, who had erythematous skin rash as a first manifesting sign of candidiasis. C tropicalis was isolated from blood and skin cultures of both patients, which were identical by pulsed-field gel electrophoresis typing. Our systematic review of outbreaks caused by C tropicalis suggests that (a) most reported outbreaks have occurred in neonatal and adult ICUs; (b) patients who receive total parenteral therapy, antibiotics and those who have indwelling catheters and recent surgery are at high risk of infection; and (c) environmental and healthcare personnel surveillance suggest that cross-contamination is a major risk factor.

CONCLUSION

Control of nosocomial outbreaks caused by C tropicalis should include better infection control measures, education of healthcare professionals especially working in adult and neonatal intensive care and haematology units.