Bacterial isolates from positive paired venous catheter and peripheral blood cultures taken during parenteral nutrition were the same species but different strains: A case report

OBJECTIVE

The same microbial species isolated from blood simultaneously drawn from a central venous catheter hub and a peripheral vein (paired blood cultures) during parenteral nutrition may be assumed to represent the same strain. This case report provides an example of this assumption being incorrect along with a comparator example of it being correct. This has implications for interpretation of differential time to positivity and differential quantitative blood cultures during investigation of suspected intraluminal intravascular catheter or cannula bloodstream infection.

CASE DESCRIPTION

Two patients ages ≥18 y prescribed parenteral nutrition each had positive paired blood cultures that had been taken for suspected catheter bloodstream infection because of temperature spikes ≥38°C. The paired Staphylococcus epidermidis isolates from the first patient and the paired Enterococcus faecium isolates from the second patient were each tested beyond routine clinical care to establish if they could be different strains. The central and peripheral isolates of Staphylococcus epidermidis from the first patient were different strains based on hospital-reported antibiograms, genomic DNA profiles, thermograms, and weaker growth and different sizes of colonies of the central strain compared with the peripheral strain. There were no such differences for the isolates of Enterococcus faecium from the second patient.

RESULTS

The central and peripheral isolates of Staphylococcus epidermidis from the first patient were different strains based on hospital-reported antibiograms, genomic DNA profiles, thermograms, and weaker growth and different sizes of colonies of the central strain compared with the peripheral strain. There were no such differences for the isolates of Enterococcus faecium from the second patient.

CONCLUSION

This case report indicates consideration should be given to reporting whether bacteria have been identified at either species or strain level if differential time to positivity or differential quantitative blood cultures are used to define catheter or cannula bloodstream infection.

Characterization of host and escherichia coli strains causing recurrent urinary tract infections based on molecular typing

BACKGROUND

Escherichia coli is the leading pathogen responsible for urinary tract infection (UTI) and recurrent UTI (RUTI). Few studies have dealt with the characterization of host and bacteria in RUTI caused by E. coli with genetically identical or different strains. This study aimed to investigate the host and bacterial characteristics of E. coli RUTI based on molecular typing.

RESULTS

Patients aged 20 years or above who presented with symptoms of UTI in emergency department or outpatient clinics between August 2009 and December 2010 were enrolled. RUTI was defined as patients had 2 or more infections in 6 months or 3 or more in 12 months during the study period. Host factors (including age, gender, anatomical/functional defect, and immune dysfunction) and bacterial factors (including phylogenicity, virulence genes, and antimicrobial resistance) were included for analysis. There were 41 patients (41%) with 91 episodes of E. coli RUTI with highly related PFGE (HRPFGE) pattern (pattern similarity > 85%) and 58 (59%) patients with 137 episodes of E. coli RUTI with different molecular typing (DMT) pattern, respectively. There was a higher prevalence of phylogenetic group B2 and neuA and usp genes in HRPFGE group if the first episode of RUTI caused by HRPFGE E. coli strains and all episodes of RUTI caused by DMT E. coli strains were included for comparison. The uropathogenic E. coli (UPEC) strains in RUTI were more virulent in female gender, age < 20 years, neither anatomical/ functional defect nor immune dysfunction, and phylogenetic group B2. There were correlations among prior antibiotic therapy within 3 months and subsequent antimicrobial resistance in HRPFGE E. coli RUTI. The use of fluoroquinolones was more likely associated with subsequent antimicrobial resistance in most types of antibiotics.

CONCLUSIONS

This study demonstrated that the uropathogens in RUTI were more virulent in genetically highly-related E. coli strains. Higher bacterial virulence in young age group (< 20 years) and patients with neither anatomical/functional defect nor immune dysfunction suggests that virulent UPEC strains are needed for the development of RUTI in healthy populations. Prior antibiotic therapy, especially the fluoroquinolones, within 3 months could induce subsequent antimicrobial resistance in genetically highly-related E. coli RUTI.

Phenotypic and genotypic characterization of Listeria monocytogenes in clinical ruminant cases in Korea

Listeria monocytogenes, a foodborne human and veterinary pathogen, is associated with high mortality rates in ruminants. However, no studies have investigated the antimicrobial resistance of L. monocytogenes isolates from clinical ruminant cases. This study aimed to determine the phenotypic and genotypic characteristics of L. monocytogenes isolates from clinical cases of Korean ruminants. We collected 24 L. monocytogenes isolates from aborted bovine fetuses and goats presenting with listeriosis-related symptoms. The isolates were subjected to PCR serogrouping, conventional serotyping, virulence gene detection, and antimicrobial susceptibility testing. Furthermore, pulsed-field gel electrophoresis and multilocus sequence typing were used to classify and compare genetic diversity among the isolates, including human L. monocytogenes isolates. The most prevalent L. monocytogenes serotypes were 4b (Ⅳ_b), 1/2a (Ⅱ_a; Ⅱ_c), and 1/2b (Ⅱ_b). All isolates harbored the virulence genes; however, llsX-encoding listeriolysin were identified only in serotypes 4b and 1/2b. All isolates, including two found in humans, formed three genetically diverse pulsed-field gel electrophoresis clusters according to serotype, lineage, and sequence type. The most prevalent sequence type was ST1, followed by ST365 and ST91. The isolates from ruminants with listeriosis were resistant to oxacillin and ceftriaxone and showed diverse lineage, serotype (serogroup), and sequence type characteristics. Considering that the atypical sequence types exhibited clinical manifestations and histopathological lesions, further study is needed to elucidate the pathogenicity of genetically diverse ruminant L. monocytogenes isolates. Furthermore, continuous monitoring of antimicrobial resistance is required to prevent the emergence of L. monocytogenes strains resistant to common antimicrobials.

Vibrio cholerae O1 El Tor strains linked to global cholera show region-specific patterns by pulsed-field gel electrophoresis

Vibrio cholerae O1 El Tor, causative agent of the ongoing seventh cholera pandemic, is native to the aquatic environment of the Ganges Delta, Bay of Bengal (GDBB). Recent studies traced pandemic strains to the GDBB and proposed global spread of cholera had occurred via intercontinental transmission. In the research presented here, NotI-digested genomic DNA extracted from V. cholerae O1 clinical and environmental strains isolated in Bangladesh during 20042014 was analyzed by pulsed-field gel electrophoresis (PFGE). Results of cluster analysis showed 94.67% of the V. cholerae strains belonged to clade A and included the majority of clinical strains of spatio-temporal origin and representing different cholera endemic foci. The rest of the strains were estuarine, all environmental strains from Mathbaria, Bangladesh, and occurred as singletons, clustered in clades B and C, or in the small clades D and E. Cluster analysis of the Bangladeshi strains and including 157 El Tor strains from thirteen countries in Asia, Africa, and the Americas revealed 85% of the total set of strains belonged to clade A, indicating all were related, yet did not form an homogeneous cluster. Overall, 15% of the global strains comprised multiple small clades or segregated as singletons. Three sub-clades could be discerned within the major clade A, reflecting distinct lineages of V. cholerae O1 El Tor associated with cholera in Asia, Africa, and the Americas. The presence in Asia and the Americas of non-pandemic V. cholerae O1 El Tor populations differing by PFGE and from strains associated with cholera globally suggests different ecotypes are resident in distant geographies.

Pyogenic liver abscess-caused Klebsiella pneumoniae in a tertiary hospital in China in 2017: implication of hypervirulent carbapenem-resistant strains

Background

To investigate the epidemiology of Klebsiella pneumoniae (K. pneumoniae) inducing pyogenic liver abscess (PLA) in east China and the role of hypervirulent carbapenem-resistant K. pneumoniae (Hv-CRKP).

Methods

Forty-three K. pneumoniae strains were collected from 43 patients with PLA at Hangzhou, China in 2017. Antimicrobial susceptibility tests, string test, multilocus sequence typing, pulsed-field gel electrophoresis, mobile genetic elements typing, regular PCR and sequencing, and Galleria mellonella (G. mellonella) lethality test were used to elucidate the epidemiology. Clinical data were collected.

Results

K. pneumoniae strains with serotypes K1 and K2 accounted for 69.8%, which shared 46.5% and 23.3% respectively. K. pneumoniae strains with clonal group 23 were predominant with a rate of 34.9%. Such antimicrobials showed susceptible rates over 80.0%: cefuroxime, cefotaxime, gentamycin, ticarcillin/clavulanate, ceftazidime, cefoperazone/tazobactam, cefepime, aztreonam, imipenem, meropenem, amikacin, tobramycin, ciprofloxacin, levofloxacin, doxycycline, minocycline, tigecycline, chloramphenicol, and trimethoprim-sulfamethoxazole. PFGE dendrogram showed 29 clusters for the 43 K. pneumoniae strains. Three Hv-CRKP strains were confirmed by G. mellonella lethality test, showing a constituent ratio of 7.0% (3/43). Totally three deaths were found, presenting a rate of 7.0% (3/43). The three died patients were all infected with Hv-CRKP.

Conclusions

K1 and K2 are the leading serotypes of K. pneumoniae causing PLA, which show highly divergent genetic backgrounds. Aminoglycosides, Generation 2^nd to 4^th cephalosporins, β-lactamase/β-lactamase inhibitors, carbapenems, fluoroquinolones are empirical choices. Hv-CRKP may confer an urgent challenge in the future.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07648-0.

Pulsed-field gel electrophoresis fingerprinting of Listeria monocytogenes isolates recovered from foods of animal origin and fishes in North-Eastern India

Listeria monocytogenes is a pathogen of great concern to the food industry. The present study was aimed to explore the clonal relationships amongst L. monocytogenes strains isolated from foods of animal origin (milk, beef, chevon (goat meat), pork and chicken) and fish. Forty-seven L. monocytogenes strains were characterized by pulsed-field gel electrophoresis (PFGE). The PFGE analysis using ApaI and AscI enzymes revealed 37 pulsotypes, with Simpson’s discriminatory index of 0.987. This study demonstrated the presence of a few similar L. monocytogenes pulsotypes in different foods of animal origin in different places and years of isolation and this indicates that some L. monocytogenes subtypes may be ubiquitous which are acclimatizing and persisting in different foods of animal origin. This also emphasizes the importance of cross-contamination in local wet markets. Thus, the understanding of genetic diversity will contribute to the development of rational and workable strategies to control this important zoonotic infection.

Karyotyping of Fusarium oxysporum by Pulsed-Field Gel Electrophoresis and the Germ Tube Burst Method

In fungi, karyotyping is fundamental to understanding their genome organization. It is also essential to study various genome- or chromosome-related topics such as karyotype polymorphisms and supernumerary or pathogenicity chromosomes. Here, we describe the protocols of pulsed-field gel electrophoresis and the germ tube burst method for molecular and cytological karyotyping of Fusarium oxysporum. The combined use of the two methods is valuable for determining definitive and comprehensive karyotypes of these fungi.

Antimicrobial Resistance and Genetic Diversity of Campylobacter spp. Isolated from Broiler Chicken at Three Levels of the Poultry Production Chain in Costa Rica

ABSTRACT

Campylobacter spp. are considered the most common bacterial cause of human gastroenteritis, one of the four main causes of diarrheal disease worldwide, and they are one of the main foodborne pathogens causing hospitalizations and deaths. Here, 148 strains of Campylobacter spp. isolated from poultry at farms, processing plants, and retail stores in Costa Rica were examined for resistance to six antibiotics. An agar dilution test was used to determine the MIC and susceptibility profiles against doxycycline, ciprofloxacin, nalidixic acid, enrofloxacin, chloramphenicol, and erythromycin. In addition, a pulsed-field gel electrophoresis analysis was carried out to determine the genotype relatedness of a representative subset of the isolates. Approximately 136 (92%) of the 148 analyzed isolates showed resistance to the tested drugs. Nalidixic acid, ciprofloxacin, and enrofloxacin were the antibiotics for which resistance occurred most frequently (91.2, 85.8, and 85.8%, respectively), followed by doxycycline (25.0%), chloramphenicol (5.4%), and erythromycin (2.7%). The profile conferring only resistance to quinolones was the most frequently found, and only 2.0% of the isolates showed resistance to quinolones and macrolides simultaneously. Results showed a high frequency of resistant Campylobacter spp. strains and evidenced the distribution, selection, and circulation of resistant strains along the poultry chain from farms to consumers. Cross-contamination and resistance seem to play important roles in the dissemination of these strains at specific points of the poultry chain, even when control measures are being taken. The establishment of effective surveillance and control strategies represents an essential tool for foodborne diseases mitigation. The rational use of antibiotics, especially those still showing efficacy, should be a priority in both human and veterinary medicine to contain the progress of this phenomenon and its consequences.

HIGHLIGHTS

Multidrug-Resistant and Extended-Spectrum β-Lactamase-Producing Salmonella enterica Serotype Heidelberg Is Widespread in a Poultry Processing Facility in Southern Brazil

ABSTRACT

This study was conducted to characterize the distribution of Salmonella isolates in a poultry processing facility and to identify their antibiotic resistance profiles. Salmonella enterica was detected in 146 samples (66.7%), and 125 isolates were identified as Salmonella Heidelberg (n = 123), Salmonella Abony (n = 1), and Salmonella O:4,5 (n = 1). Salmonella Heidelberg isolates were subjected to XbaI macrorestriction analysis and pulsed-field gel electrophoresis. The 66 pulsotypes obtained were grouped into four major clusters, indicating cross-contamination and persistence of this serotype in the processing facility. Selected S. enterica isolates were characterized by their antibiotic resistance, and most (n = 122, 97.6%) were multidrug resistant. Resistance to third-generation cephalosporins ceftazidime (84 isolates, 67.2%) and cefotaxime and ceftriaxone (91 isolates, 72.8%) was particularly prevalent. Production of extended-spectrum β-lactamases (ESBL) was identified in 24 isolates (19.2%), and ESBL-producing isolates were resistant to at least eight antibiotics. This study revealed the high prevalence of Salmonella Heidelberg in the poultry chain, providing insight into the ecology of this pathogen in this facility. The high prevalence of multidrug-resistant S. enterica is a concern due to the potential consequences for public health.

HIGHLIGHTS

Nosocomial infections caused by vancomycin-resistant Enterococcus in a Japanese general hospital and molecular genetic analysis

INTRODUCTION

Vancomycin-resistant Enterococcus (VRE) is a rare bacterium in Japan, but an outbreak due to nosocomial transmission in medical facilities has been reported in recent years. Here, we report the outbreak of vanA vancomycin-resistant Enterococcus faecium (VREfm) in multiple wards of Nara Prefectural General Medical Center in 2019 and results of the molecular epidemiology analysis.

METHODS

An aggressive screening program was conducted after the first VREfm was detected in a patient in the A ward. During the outbreak, 6000 rectal swab samples were screened for VRE by culture. Isolates from 60 patients with VREfm detected were clustered using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).

RESULTS

PFGE revealed a cluster consisting of three major clusters and four multi-strains. The first major cluster consisted of 26 isolates, the second consisted of 10 isolates, the third consisted of 6 isolates, and the remaining 4 clusters consisted of 2 isolates. MLST identified an allele profile (ST80) in most clusters of clone types P01-P06 but an allele profile (ST992) in cluster P07.

CONCLUSION

Based on the PFGE pattern, this case was considered to be a nosocomial infection due to multiple clones. Later, in addition to screening, sharing of hospital information, cohorting of patients and staff, and strengthening of environmental cleanup were carried out, and horizontal infection was suppressed.

Determining the DNA Fingerprinting Profiles of Salmonella Isolates from Raw Poultry Meats and Human Clinical Samples from the Same Geographic Area Using Pulsed-Field Gel Electrophoresis

ABSTRACT

Foods of animal origin, such as poultry, eggs, and pork, are recognized sources of Salmonella infections, but determination of the proportion of foodborne infections associated with various food sources has been challenging. In the present study, 141 Salmonella isolates recovered from 1,322 poultry product samples purchased over a 1-year period from retail stores across Seattle, WA were subtyped by pulsed-field gel electrophoresis (PFGE) using restriction enzyme XbaI. The objectives of the study were (i) to analyze the longitudinal distribution of Salmonella PFGE profiles throughout the sampling period and their clonality within and between poultry processing establishments, (ii) to determine the association between PFGE profiles of Salmonella isolates from locally distributed poultry products and those of clinical isolates submitted to the Washington State Department of Health (WA-DOH) laboratories, and (iii) to compare the PFGE profiles of Salmonella isolates from the National Antimicrobial Resistance Monitoring System (NARMS) retail meats program. During the 1-year sampling period, multiple indistinguishable PFGE patterns were found across multiple poultry processing establishments. Twelve of the 30 unique PFGE profiles of Salmonella isolates from locally purchased poultry products were indistinguishable from the PFGE profiles of clinical Salmonella isolates submitted to the WA-DOH. When the PFGE profiles from the poultry samples were compared with those found in the NARMS database, eight indistinguishable PFGE matches were found with isolates recovered from chicken breasts, ground turkey, and ground beef from multiple states. Although this study revealed some association between PFGE profiles from raw poultry products and those of clinical isolates from the same geographical area, these results do not prove that all of those clinical isolates were from infections acquired through consumption or handling of poultry.

HIGHLIGHTS

Genetic diversity assessed using PFGE, MLP and MLST in Candida spp. candidemia isolates obtained from a Brazilian hospital

Candida spp. are the main causative agents of invasive fungal infections in immunocompromised patients. Candidemia has attributable mortality rates of 15 to 35% and increases hospitalisation time and costs, thus making this disease a public health concern. This study aimed to use pulsed-field gel electrophoresis (PFGE), microsatellite length polymorphism (MLP) and multilocus sequence typing (MLST) to analyse the genetic relationships among 65 Candida spp. bloodstream isolates, including 35 Candida albicans, 15 Candida glabrata and 15 Candida tropicalis isolates, all of which were obtained from patients in a Brazilian hospital. Moreover, patient clinical data were assessed. All techniques resulted in high discriminatory indexes. C. albicans and C. tropicalis isolates showed high genetic variability, while C. glabrata isolates had relatively low genetic variability. Moreover, a cluster of C. glabrata isolates was identified in a hospital unit. New MLST sequence types, diploid sequence types and alleles are described. Relationships were not observed between the molecular typing results and clinical characteristics. The molecular typing of clinical strains increases our understanding of candidemia epidemiology and promotes the development of strategies that can reduce the incidence of this disease. Moreover, this study is the first to combine these techniques to genotype these three species in Brazil.

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.

Analysis of virulence genes and molecular typing of Listeria monocytogenes isolates from human, food, and livestock from 2008 to 2016 in Iran

The frequency of Listeria monocytogenes isolates collected from a total of 1150 samples including food (n = 300), livestock (n = 50), and human clinical (n = 800) was evaluated during 2008-2016. Antimicrobial resistance patterns, virulence factors, and molecular characteristics of these isolates were analyzed using disk diffusion method, sequencing, serotyping, and pulsed-field gel electrophoresis (PFGE). The analysis of 44 L. monocytogenes isolates showed that 72.7% (32 of 44) of all the isolates belonged to Serotype 1/2c, and 15.9% (7 of 44) belonged to Serotype 3c. All 44 isolates were resistant to one or more antimicrobial agents with the most frequent resistance to penicillin (75%) and tetracycline (47.7%). Of the 44 L. monocytogenes strains, 100, 69.2, and 62.5% of livestock, human, and food strains were resistant to penicillin, respectively. Using pulsed-field gel electrophoresis (PFGE) technique, the isolates' genetic diversity was determined, and 28 PFGE patterns with 8 common (CT) and 20 single types (ST) were identified. This study highlights the high prevalence of Serotype 1/2c in clinical and livestock samples, while different serotypes were observed in food samples. The presence of rare serotypes such as 4c, belonging to the Lineage III, as well as 4e and 1/2c which are infrequent in Iran indicates that paying attention to uncommon serotypes, especially 1/2c, during the listeriosis outbreaks is necessary.

Highly prevalent multidrug resistance and QRDR mutations in Salmonella isolated from chicken, pork and duck meat in Southern China, 2018-2019

This study was undertaken to investigate the prevalence, serotype distribution and antimicrobial resistance in Salmonella isolated from retail meat in Southern China, and to characterize the major mechanisms that mediate the ciprofloxacin resistance of isolates. High levels of Salmonella contamination were detected in pork (67.0%), duck (50.5%) and chicken (46.2%). Thirty different serotypes were identified among 500 detected Salmonella isolates, as well as significant differences in serotypes between different retail meat samples. Notably, 405 (80.1%) isolates exhibited multidrug resistance (MDR). Meanwhile, we also found that 74 (14.8%) Salmonella isolates were resistant to ciprofloxacin and the major mechanisms underlying this resistance were investigated. The commonest mutations in gyrA S83F (40.5%) and D87N (35.1%), and in parC was T57S (71.6%) and S80I (35.1%). Multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) analysis revealed that the S. Kentucky isolates that were resistant to ciprofloxacin mostly belonged to ST198 (21/23, 91.3%) and PFGE revealed the presence of various genotypes. This study identified a diversity of Salmonella serotypes and a high prevalence of multidrug resistance (MDR) among Salmonella isolated from retail meat in Southern China, which indicates that foodborne Salmonella potentially constitutes a potential food safety risk.

Isolation and Visualization of Plasmids from Gram-Positive Bacteria of Interest in Public Health

This chapter describes the methods to extract and characterize plasmids of Gram-positive bacterial species of interest in public health (biomedicine, veterinary, and food safety) as Staphylococcus, Streptococcus, Enterococcus, Listeria, and Clostridium and lactic acid bacteria. References for detailed plasmid classification are given in order to provide a comprehensive landscape in the interpretation of their plasmidomes.

Plasmid DNA Isolation and Visualization: Isolation and Characterization of Plasmids from Clinical Samples

Plasmids are important in carrying antibiotic resistance and other genes between bacterial cells, and a number of methods can be employed to characterize plasmids from clinical isolates. Single colonies typically obtained as part of hospital workflow can undergo S1 nuclease treatment to linearize plasmids followed by pulsed-field gel electrophoresis to enable determination of the number and sizes of plasmids present. Hybridization of S1/PFGE gels can be used to associate replicon types and passenger genes, such as those conferring antibiotic resistance, with a particular plasmid band. Individual plasmids, obtained by conjugation or transformation, can be compared by gel electrophoresis following restriction digestion of plasmid DNA prepared by alkaline lysis methods, including using specialized kits.

Gel Electrophoresis Analysis of rDNA Instability in Saccharomyces cerevisiae

The ribosomal RNA (rDNA) sequence is the most abundant repetitive element in the budding yeast genome and forms a tandem cluster of ~100-200 copies. Cells frequently change their rDNA copy number, making rDNA the most unstable region in the budding yeast genome. The rDNA region experiences programmed replication fork arrest and subsequent formation of DNA double-strand breaks (DSBs), which are the main drivers of rDNA instability. The rDNA region offers a unique system to understand the mechanisms that respond to replication fork arrest as well as the mechanisms that regulate repeat instability. This chapter describes three methods to assess rDNA instability.

Small Produce Farm Environments Can Harbor Diverse Listeria monocytogenes and Listeria spp. Populations

ABSTRACT

A comprehensive understanding of foodborne pathogen diversity in preharvest environments is necessary to effectively track pathogens on farms and identify sources of produce contamination. As such, this study aimed to characterize Listeria diversity in wildlife feces and agricultural water collected from a New York state produce farm over a growing season. Water samples were collected from a pond (n = 80) and a stream (n = 52). Fecal samples (n = 77) were opportunistically collected from areas <5 m from the water sources; all samples were collected from a <0.5-km2 area. Overall, 86 (41%) and 50 (24%) of 209 samples were positive for Listeria monocytogenes and Listeria spp. (excluding L. monocytogenes), respectively. For each positive sample, one L. monocytogenes or Listeria spp. isolate was speciated by sequencing the sigB gene, thereby allowing for additional characterization based on the sigB allelic type. The 86 L. monocytogenes and 50 Listeria spp. isolates represented 8 and 23 different allelic types, respectively. A subset of L. monocytogenes isolates (n = 44) from pond water and pond-adjacent feces (representing an ∼5,000-m2 area) were further characterized by pulsed-field gel electrophoresis (PFGE); these 44 isolates represented 22 PFGE types, which is indicative of considerable diversity at a small spatial scale. Ten PFGE types were isolated more than once, suggesting persistence or reintroduction of PFGE types in this area. Given the small spatial scale, the prevalence of L. monocytogenes and Listeria spp., as well as the considerable diversity among isolates, suggests traceback investigations may be challenging. For example, traceback of finished product or processing facility contamination with specific subtypes to preharvest sources may require collection of large sample sets and characterization of a considerable number of isolates. Our data also support the adage "absence of evidence does not equal evidence of absence" as applies to L. monocytogenes traceback efforts at the preharvest level.

HIGHLIGHTS

Shiga Toxin-Producing E. coli in Animals: Detection, Characterization, and Virulence Assessment

Cattle and other ruminants are primary reservoirs for Shiga toxin-producing Escherichia coli (STEC) strains which have a highly variable, but unpredictable, pathogenic potential for humans. Domestic swine can carry and shed STEC, but only STEC strains producing the Shiga toxin (Stx) 2e variant and causing edema disease in piglets are considered pathogens of veterinary medical interest. In this chapter, we present general diagnostic workflows for sampling livestock animals to assess STEC prevalence, magnitude, and duration of host colonization. This is followed by detailed method protocols for STEC detection and typing at genetic and phenotypic levels to assess the relative virulence exerted by the strains.

Antibiotic Resistance Characteristics and Prevalence in Kitfo, an Ethiopian Beef Tartar

ABSTRACT

Kitfo is a version of beef tartar widely consumed in the Ethiopian community. It is made from raw minced beef and a blend of powdered spice and butter. Although previous studies have shown that kitfo contains several bacteria that are of public health concern, the status of their antibiotic resistance is not known. In this study, the antibiotic resistance of bacterial isolates from 26 retail kitfo samples obtained from the Washington metropolitan area was analyzed. Characterization and antibiotic sensitivity of the isolates were determined by the Vitek 2 system and pulsed-field gel electrophoresis was used to delineate the intraspecies variations. Of the isolates, 59% were resistant to two or more antibiotics. Acinetobacter calcoaceticus and Pseudomonas luteola were multidrug resistant to the classes of β-lactam, cephalosporins, and nitrofurantoin. The antibiotic susceptibility profile of the isolates was cefazolin (59%), cefoxitin (50%), ampicillin (32%), and nitrofuran (18%). Most isolates (75%) were Enterobacteriaceae, whereas only 3.8 and 2.6% were Pseudomonadaceae and Moraxellaceae, respectively. Of the Enterobacteriaceae, Enterobacter cloacae, Escherichia coli, and Klebsiella spp. were the most predominant. All isolates except Klebsiella spp. showed high genetic variation (>65%). This study implicates for the first time kitfo as a potential reservoir of antibiotic-resistant bacteria.

HIGHLIGHTS

Emergence of optrA-Mediated Linezolid-Nonsusceptible Enterococcus faecalis in a Tertiary Care Hospital

This study investigated resistance mechanisms and epidemiology of emerging linezolid-nonsusceptible Enterococcus faecalis (LNSEF) in a tertiary care hospital. LNSEF isolated from clinical samples were collected from November 2017 to June 2019. The isolates were investigated for linezolid resistance and the associated molecular mechanisms, including mutations of 23S rRNA domain V and acquisition of the cfr or optrA resistance gene. We used pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing for the molecular typing of the isolates. Among 4,318 E. faecalis isolates, 10 (0.23%) were linezolid-nonsusceptible. All LNSEF isolates were optrA-positive and cfr-negative. Of these isolates, five were sequence type (ST) 476, two ST585, one ST16, one ST16-like, and one ST480. Six LNSEF isolates obtained in the first year clustered to three types in the PFGE analysis: two ST476 isolates of type A, two ST585 isolates of type B, and two ST16 or ST16-like isolates of type C. Seven cases were of community-onset and three were hospital acquired, but total of eight were healthcare-associated including five community-onset. None of the patients had a history of linezolid treatment, and in one patient, we detected linezolid-susceptible E. faecalis one month before LNSEF detection. In conclusion, heterogenous clones of optrA-positive LNSEF emerged in the hospital mainly via community-onset.

Clinical perspectives in integrating whole-genome sequencing into the investigation of healthcare and public health outbreaks - hype or help?

Outbreaks pose a significant risk to patient safety as well as being costly and time consuming to investigate. The implementation of targeted infection prevention and control measures relies on infection prevention and control teams having access to rapid results that detect resistance accurately, and typing results that give clinically useful information on the relatedness of isolates. At present, determining whether transmission has occurred can be a major challenge. Conventional typing results do not always have sufficient granularity or robustness to define strains unequivocally, and sufficient epidemiological data are not always available to establish links between patients and the environment. Whole-genome sequencing (WGS) has emerged as the ultimate genotyping tool, but has not yet fully crossed the divide between research method and routine clinical diagnostic microbiological technique. A clinical WGS service was officially established in 2014 as part of the Scottish Healthcare Associated Infection Prevention Institute to confirm or refute outbreaks in hospital settings from across Scotland. This article describes the authors' experiences with the aim of providing new insights into practical application of the use of WGS to investigate healthcare and public health outbreaks. Solutions to overcome barriers to implementation of this technology in a clinical environment are proposed.

Listeria monocytogenes Prevalence Varies More within Fields Than between Fields or over Time on Conventionally Farmed New York Produce Fields

ABSTRACT

Past studies have shown that the on-farm distribution of Listeria monocytogenes is affected by environmental factors (e.g., weather). However, most studies were conducted at large scales (e.g., across farms), whereas few studies examined drivers of L. monocytogenes prevalence at smaller scales (e.g., within a single field). This study was performed to address this knowledge gap by (i) tracking L. monocytogenes distribution in two fields on one farm over a growing season and (ii) identifying factors associated with L. monocytogenes isolation from drag swab, soil, and agricultural water samples. Overall, L. monocytogenes was detected in 78% (21 of 27), 19% (7 of 36), and 8% (37 of 486) of water, drag swab, and soil samples, respectively. All isolates were characterized by pulsed-field gel electrophoresis. Of the 43 types identified, 14 were isolated on multiple sampling visits and/or from multiple sample types, indicating persistence in or repeated introduction into the farm environment during the study. Our findings also suggest that L. monocytogenes prevalence, even at the small spatial scale studied here, (i) was not uniform and (ii) varied more within fields than between fields or over time. This is illustrated by plot (in-field variation), field (between-field variation), and sampling visit (time), accounting for 18, 2, and 3% of variance in odds of isolating L. monocytogenes, respectively. Moreover, according to random forest analysis, water-related factors were among the top-ranked factors associated with L. monocytogenes isolation from all sample types. For example, the likelihood of isolating L. monocytogenes from drag and soil samples increased monotonically as rainfall increased. Overall, findings from this single-farm study suggests that mitigation strategies for L. monocytogenes in produce fields should focus on water-associated risk factors (e.g., rain and distance to water) and be tailored to specific high-risk in-field areas.

HIGHLIGHTS

Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia

We sought to determine the relative value of conventional molecular methods and whole-genome sequencing (WGS) for subtyping Salmonella enterica serovar Enteritidis recovered from 2000 to 2015 in Tunisia and to investigate the genetic diversity of this serotype. A total of 175 Salmonella Enteritidis isolates were recovered from human, animal, and foodborne outbreak samples. Pulsed-field gel electrophoresis (PFGE), multiple locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing were performed. Eight pulsotypes were detected for all isolates with PFGE (DI = 0.518). Forty-five Salmonella Enteritidis isolates were selected for the MLVA and WGS techniques. Eighteen MLVA profiles were identified and classified into two major clusters (DI = 0.889). Core genome multilocus typing (cgMLST) analysis revealed 16 profiles (DI = 0.785). Whole-genome analysis indicated 660 single-nucleotide polymorphism (SNP) divergences dividing these isolates into 43 haplotypes (DI = 0.997). The phylogenetic tree supported the classification of Salmonella Enteritidis isolates into two distinct lineages subdivided into five clades and seven subclades. Pairwise SNP differences between the isolates ranged between 302 and 350. We observed about 311 SNP differences between the two foodborne outbreaks, while only less or equal to 4 SNP differences within each outbreak. SNP-based WGS typing showed an excellent discriminatory power comparing with the conventional methods such as PFGE and MLVA. Besides, we demonstrate the added value of WGS as a complementary subtyping method to discriminate outbreak from non-outbreak isolates belonging to common subtypes. It is important to continue the survey of Salmonella Enteritidis lineages in Tunisia using WGS.

Antimicrobial resistance and molecular characterization of Salmonella enterica serovar Corvallis isolated from human patients and animal source foods in China

In this study, 205 Salmonella enterica serovar Corvallis strains were obtained from humans and foods from Guangdong, Guangxi, and Shanghai in China from 2009 to 2017 to assess drug resistance and molecular epidemiology. These isolates displayed high rates of resistance to sulfisoxazole (94.15%) and tetracycline (77.56%). Surprisingly, the rate of resistance to ciprofloxacin reached 21.46%. Moreover, 63.9% of the strains displayed multidrug resistance. Detection of quinolone genes showed that 97.56% of the strains had single mutations (T57S) in parC. The plasmid-mediated quinolone resistance (PMQR) genes qnrS, aac(6')-Ib-cr, and qnrB, were also detected. The extended spectrum β-lactamase (ESBLS) gene that was most common among the isolates was bla_TEM-1 (18.05%). These S. Corvallis isolates are the first to date, that have been reported to possess bla_CTX-M-55 or bla_NDM-5. Additionally, 95.61% of isolates were biofilm producers. The streptomycin resistance rate was higher in strong biofilm producers (87.50%) than in moderate (37.93%) and weak (26.49%) biofilm producers. Pulsed-field gel electrophoresis (PFGE) showed that some strains from different sources had the same genotype. These isolates may be transmitted to humans through food and therefore the monitoring of these isolates should be strengthened in China.

Investigation of a salmonellosis outbreak linked to French toast sandwich with the use of surveillance camera, Taiwan, 2018

Salmonella is a leading cause of foodborne outbreaks in Taiwan. On 27 April 2018, a salmonellosis outbreak among customers of a restaurant was reported to the Taiwan CDC. We investigated the outbreak to identify infection sources and prevent further transmission. We interviewed ill customers and their dining companions. We conducted a case-control study to identify foods associated with the illness. Case-patients were those who had diarrhoea within 72 h after eating at the restaurant during 16–27 April 2018. Specimens, food samples and environmental samples were collected and tested for enteric pathogens. Salmonella isolates were analysed with pulse-field gel electrophoresis and whole-genome sequencing. We inspected the restaurant sanitation and reviewed kitchen surveillance camera recordings. We identified 47 case-patients, including one decedent. Compared with 44 controls, case-patients were more likely to have had a French toast sandwich (OR: 102.4; 95% CI: 18.7–952.3). Salmonella Enteritidis isolates from 16 case-patients shared an indistinguishable genotype. Camera recordings revealed eggshell contamination, long holding time at room temperature and use of leftovers during implicated food preparation. Recommendations for restaurant egg-containing food preparation are to use pasteurised egg products and ensure a high enough cooking temperature and long enough cooking time to prevent Salmonella contamination.

Prevalence, genotypic diversity and detection of virulence genes in thermotolerant Campylobacter at different stages of the poultry meat supply chain

Thermotolerant Campylobacter is the leading bacterial cause of foodborne illness in humans worldwide. The objectives of this study were to estimate prevalence and to identify and characterize potential sources of thermotolerant Campylobacter contamination in broilers on farms and at the slaughterhouse; to evaluate the clonal relationship among thermotolerant Campylobacter isolates from different stages of the broiler meat supply chain, and to analyze the presence of virulence genes in different sources of thermotolerant Campylobacter. A total of 1210 samples were collected from three broiler meat supply chains in Santa Fe, Argentina. At the farms, the sampling collection included broilers one week prior to slaughter, wild-living birds, domestic dogs, wild rodents, farm workers' boots, litter, feed, drinking water, flies, and darkling beetles (Alphitobius diaperinus). At the slaughtering line, the samples taken were from the evisceration zone (broiler cecum, working surfaces, evisceration knives and workers' hands), from the chiller zone (surfaces and direct supply water) and from the packing zone (work surfaces, workers' hands and broiler carcasses). The samples taken along each supply chain were in the same batch. The isolates obtained were identified to the species level (C. jejuni and C. coli) by multiplex PCR and were analyzed using pulsed-field gel electrophoresis to compare different profiles according to the source. Finally, the presence of 11 virulence genes was examined (cadF, cdtA, cdtB, cdtC, ciaB, flaA, flhA, iam, wlaN, virB11, racR). From 254 isolates, 128 (50.4%) were Campylobacter jejuni and 126 (49.6%) Campylobacter coli. C. jejuni was the species most prevalent in farm and C. coli the species most prevalent at the slaughterhouse. We detected thermotolerant Campylobacter in samples of wild birds, darkling beetles, farm workers' boots, flies and litter. At the slaughterhouse, the prevalence varied along the process line. By analyzing PFGE results, C. jejuni showed 21 profiles with three predominant genotypes, while C. coli showed 14 profiles with four predominant genotypes. A high genotype diversity was found; however, relationships between isolates from different stages of the broiler meat chain, between broiler and potential sources of thermotolerant Campylobacter contamination and between strains in the farm and in the slaughterhouse were detected. Furthermore, there was evidence of cross-contamination at the slaughterhouse. FlaA, flhA genes were detected in all strains, and the third most prevalent virulence gene was cadF. Only those strains obtained from flies, wild-living birds and broiler carcass samples harbored 10 of 11 pathogenic genes. The prevalence of some pathogenic genes between C. jejuni and C. coli was different. This evidence should contribute the scientific basis to implement risk management measures in public health.

Genetic and virulence characterisation of Vibrio parahaemolyticus isolated from Indian coast

BACKGROUND

V. parahaemolyticus is autochthonous to the marine environment and causes seafood-borne gastroenteritis in humans. Generally, V. parahaemolyticus recovered from the environment and/or seafood is thought to be non-pathogenic and the relationship between environmental isolates and acute diarrhoeal disease is poorly understood. In this study, we explored the virulence potential of environmental V. parahaemolyticus isolated from water, plankton and assorted seafood samples collected from the Indian coast.

RESULTS

Twenty-two V. parahaemolyticus isolates from seafood harboured virulence associated genes encoding the thermostable-direct haemolysin (TDH), TDH-related haemolysin (TRH), and Type 3 secretion systems (T3SS) and 95.5% of the toxigenic isolates had pandemic strain attributes (toxRS/new+). Nine serovars, with pandemic strain traits were newly identified and an O4:K36 tdh-trh+V. parahaemolyticus bearing pandemic marker gene was recognised for the first time. Results obtained by reverse transcription PCR showed trh, T3SS1 and T3SS2β to be functional in the seafood isolates. Moreover, the environmental strains were cytotoxic and could invade Caco-2 cells upon infection as well as induce changes to the tight junction protein, ZO-1 and the actin cytoskeleton.

CONCLUSION

Our study provides evidence that environmental isolates of V. parahaemolyticus are potentially invasive and capable of eliciting pathogenic characteristics typical of clinical strains and present a potential health risk. We also demonstrate that virulence of this pathogen is highly complex and hence draws attention for the need to investigate more reliable virulence markers in order to distinguish the environmental and clinical isolates, which will be crucial for the pathogenomics and control of this pathogen.

PCR-Restriction Fragment Length Polymorphism and Pulsed-Field Gel Electrophoresis Characterization of Listeria monocytogenes Isolates from Ready-to-Eat Foods, the Food Processing Environment, and Clinical Samples in South Africa

ABSTRACT

Listeria monocytogenes is a ubiquitous, intracellular foodborne pathogen that is responsible for invasive listeriosis. The ability of L. monocytogenes to cause disease has some correlation with the serotypes of a specific lineage group, making the identification of lineage groups important for epidemiological analysis. The development of typing methods to link the strains of L. monocytogenes to an outbreak of listeriosis would help minimize the spread of the disease. The aim of this study was to design a PCR-restriction fragment length polymorphism (RFLP) method to differentiate between the lineage groups of L. monocytogenes. PCR-amplified fragments of the hly gene for 12 serotypes of L. monocytogenes were sequenced, aligned, and analyzed with the BioEdit program, and single nucleotide polymorphisms (SNPs) within regions of this gene were identified. Because of the difficulty in acquiring a serotype 4ab reference strain, this serotype was not included in this study. We tested the specificity and accuracy of the PCR-RFLP method on these L. monocytogenes reference strains and validated the method with 172 L. monocytogenes strains recovered from humans, food, and the food processing environment in 2000 to 2002 and 2008 to 2010 from regions within South Africa. PCR-RFLP analysis applied in this study placed L. monocytogenes serotypes into one of three lineage groups based on the sequence differences and SNPs within each lineage group. The SNPs were conserved in a region where RFLP analysis could be applied for a distinction between L. monocytogenes lineage groups.

HIGHLIGHTS

Genome diversity and evolutionary characteristics of clinical isolates of Bordetella pertussis circulating in Iran

BACKGROUND AND OBJECTIVES

The re-emergence of pertussis still is being reported all over the world. Pathogen adaptation and antigenic divergence of circulating isolates from vaccine strains are the main reasons of infection resurgence. Waning immunity is also an important factor contributing to resurgence of pertussis.

MATERIALS AND METHODS

The genetic diversity and evolutionary characteristics of circulating Iranian isolates of Bordetella pertussis during February 2015 to October 2018 was investigated by pulsed-field gel electrophoresis (PFGE) and subsequently ptxA, ptxP and fim3 alleles were characterized. The next generation genome sequencing was then used to compare the genomics of ptxP1 and ptxP3 of selected isolates from PFGE dendrogram.

RESULTS

PFGE differentiated 62 clinical isolates and vaccine and reference strains into 19 PFGE profiles, indicating the higher level of heterogeneity in the population during 2015-2018. The predominant B. pertussis genotype harbored pertussis toxin promoter allele, ptxP3 and the expansion of ptxA1 isolates, were also observed in our population.

CONCLUSION

No changes in allelic profile of predominant clone in recent years was observed but antigenic divergence between recently circulating isolates and the vaccine strain has been progressed and significantly was higher than previous studies. The comparative genomic analysis of the ptxP3 and ptxP1 isolates indicate that changes in ptxP3 genome structure including 32 unique SNPs and three unique indels may have contributed to the expansion of the ptxP3 clone. We compared ptxP3 and ptxP1 isolates in pathogenicity-associated genes and found five of them were specific for the ptxP3 isolates. The polymorphisms in pathogenicity-associated genes suggest structural adaptations for these virulence factors.

Code and data on the processing of the pulsed-field gel electrophoresis images: A matlab script

Here a matlab script was presented for lane tracking and band detection on the pulsed field gel electrophoresis (PFGE) images. It can also be used as a software tool for automatic analysis of PFGE images. The data consist of several MATLAB codes which collectively have the task of lane tracking, band detecting and pattern recognition on the PFGE images. The lane tracking stage is semi-automatic and the band detection stage is fully automatic. Finally, the pattern of lanes that includes number of, location, width and light intensity level of bands was obtained.

Pulsed-Field Gel Electrophoresis Typing of Staphylococcus aureus Strains

Pulsed-field gel electrophoresis (PFGE) is one of the most effective genotyping methods for the study of genetic relatedness of microorganisms as well as for epidemiologic investigation of outbreaks caused by pathogenic bacteria, including Staphylococcus aureus. The technique relies on the size patterns of large DNA fragments generated by the cleavage of intact bacterial chromosomes with a rare cutting restriction enzyme, and subsequently resolved by pulsed-field electrophoresis with periodic changes of the orientation of the electrical field across the gel. The high discriminatory power, improved reproducibility by standardization of experimental protocols and data analysis guidelines, and establishment of a national PFGE database of S. aureus profiles have made it a valuable means for global tracking of S. aureus infection sources and determination of genetic relatedness of the strains.

Introduction and Perspectives of DNA Electrophoresis

Gel electrophoresis of DNA is one of the most frequently used techniques in molecular biology. Typically, it is used in the following: the analysis of in vitro reactions and purification of DNA fragments, analysis of PCR reactions, characterization of enzymes involved in DNA reactions, and sequencing. With some ingenuity gel electrophoresis of DNA is also used for the analysis of cellular biochemical reactions. For example, DNA breaks that accumulate in cells are analyzed by the comet assay and pulsed-field gel electrophoresis (PFGE). Furthermore, DNA replication intermediates are analyzed with two-dimensional (2D) gel electrophoresis. Moreover, several new methods for analyzing various chromosomal functions in cells have been developed. In this chapter, a brief introduction to these is given.

Predictors for vancomycin resistant Enterococcus faecium transforming from colonization to infection: a case control study

Background

Little is known about risk factors for subsequent infections among vancomycin resistant Enterococcus faecium (VREfm) colonizers, especially characterized by concordant pulsotypes (CP) of paired colonization and infection-related isolates.

Methods

This case-control study was conducted at a teaching hospital between 2011 and 2014. Targeted patients received active surveillance culture for VREfm by anal swabs at admission. Cases were those who developed VREfm infection within 180 days after colonization of VREfm. Controls were those colonized with VREfm without subsequent VREfm infection. CP were defined by similarities ≥86.7% using pulsed-field gel electrophoresis between paired colonization and infection-related isolates.

Results

Ninety-seven cases and 194 controls were enrolled. By conditional multivariable logistic regression analysis, the risk factors for subsequent infection among VREfm colonizers were intensive care unit (ICU) admission (adjusted odds ratio [aOR], 9.32; 95% CI, 3.61–24.02), receipt of central venous catheters (CVC) (aOR, 3.38; 95% CI, 1.30–8.82), and utilization of third- and fourth-generation cephalosporins (aOR, 4.06; 95% CI, 1.79–9.20, and aOR, 5.32; 95% CI, 1.85– 10.29, respectively) (all P ≤ 0.01). Fifty-six (57.7%) of case patients belonged to the CP group, which were associated with ICU admission (aOR, 3.74; 95% CI, 1.38–10.13), and infection developing within 30 days after colonization (aOR, 3.34; 95% CI, 1.25–8.91).

Conclusions

Among VREfm colonizers, being admitted to ICU and receiving CVC or broad spectrum cephalosporins, were the risk factors for subsequent infections. These findings highlight the importance of conducting more strict infection control measures on specific groups of VREfm colonizers.

Population structure and transmission modes of indigenous typhoid in Taiwan

BACKGROUND

Indigenous typhoid fever was continuing to be identified in Taiwan which has not been endemic for the enteric fever for more than 20 years. The source and transmission by which the local patients acquired typhoid and the population structure of the indigenous typhoid strains remain not well characterized.

METHODS

During 2001 and 2014, non-duplicated clinical Salmonella enterica serovar Typhi isolates in a hospital were analyzed by whole-genome sequencing (WGS) and determined for pulsotypes. Maximum likelihood phylogeny was constructed by nucleotide alterations in core genomes and compared to the framework of global typhoid strains. Potential source and transmission were traced by correlating the phylogeny and the temporal relationship between isolates.

RESULTS

A total of 43 S. Typhi isolates from indigenous cases were analyzed and a majority (39, 90.7%) of them were belonged to six WGS-defined genotypes prevailing mainly in Southeast Asia. Genotype 3.4.0 and a multidrug-resistant type 4.3.1 (also known as pandemic H58 haplotype) were associated respectively with two solitary small-scale outbreaks, implying a transmission mode of importation followed by outbreak. Twelve isolates with nearly identical core genomes were belonged to genotype 3.2.1 but were categorized into three different pulsotypes. The 3.2.1 isolates were identified across 13 years and involved in three clusters and a sporadic case, indicating sustained local transmission of the same strain. The remaining indigenous isolates belonging to three genotypes (2.1, 3.1.2, and 3.0.0) were of substantial genetic diversity and isolated at different time points, indicating independent event of each case.

CONCLUSIONS

Indigenous typhoid in Taiwan occurred mainly with the forms of small-scale outbreaks or sporadic events likely by contracting imported strains which prevailed in Southeast Asia. Sustained local transmission of certain strain was also evident by WGS analysis, but not by conventional pulsotyping, highlighting the importance of continuing molecular surveillance of typhoid fever with adequate tools in the non-endemic region.

Detection of DNA Double-Strand Breaks Using Pulsed-Field Gel Electrophoresis

DNA is one of the most biologically important targets of exogenous and endogenous toxicants as well as carcinogens. Damage to DNA can be of different types (e.g., DNA adducts, DNA protein cross-links, single-strand breaks, oxidized bases, abasic sites, and double-strand breaks (DSBs)). DSBs are considered the most lethal form of DNA damage for eukaryotic cells, and if left unrepaired or misrepaired, can cause cell death, chromosome instability, and cancer. DSBs can arise in the cells through different sources and can be distinguished as endogenous or exogenous DSBs. Exogenous sources can be chemotherapeutic drugs, irradiation, and environmental chemicals. The endogenous causes of DNA DSBs in the cells are mainly reactive oxygen species and faulty repair of oxidative clustered DNA lesions. Qualitative and quantitative analysis of DNA DSBs is of utmost importance to understand physiologically relevant cellular processes as well as to investigate the genotoxic or clastogenic effects of toxicants. Pulsed-field gel electrophoresis (PFGE) is a widely used method for direct quantification of DNA DSBs. In this method, the cells exposed to DSB-inducing agents are embedded in the agarose blocks and lysed. These agarose blocks containing DNA are then run under multiple electric fields which are at 120° angle, to aid in the movement of large DNA strands. It gives a direct and specific measure of DSBs unlike the foci-based assays. This chapter provides a brief overview of the various commonly used approaches to analyze DNA DSBs and describes the theory, advantages and method of PFGE, for use in cells exposed to DNA DSB inducing agents.

The population structure of Ochrobactrum isolated from entomopathogenic nematodes indicates interactions with the symbiotic system

Entomopathogenic nematodes (EPNs) form specific mutualistic associations with bioluminescent enterobacteria. In Heterorhabditidis indica, Ochrobactrum spp. was identified beside the symbiont Photorhabdus luminescens but its involvement in the symbiotic association in the EPNs remains unclear. This study describe the population structure and the diversity in Ochrobactrum natural populations isolated from EPNs in the Caribbean basin in order to question the existence of EPN-specialized clones and to gain a better insight into Ochrobactrum-EPNs relationships. EPN-associated Ochrobactrum and Photorhabdus strains were characterized by multi-locus sequence typing, Pulsed-Field Gel Electrophoresis fingerprinting and phenotypic traits. Population study showed the absence of EPN-specialized clones in O. intermedium and O. anthropi but suggested the success of some particular lineages. A low level of genetic and genomic diversification of Ochrobactrum isolated from the natural population of Caribbean nematodes was observed comparatively to the diversity of human-associated Ochrobactrum strains. Correspondences between Ochrobactrum and P. luminescens PFGE clusters have been observed, particularly in the case of nematodes from Dominican Republic and Puerto Rico. O. intermedium and O. anthropi associated to EPNs formed less biofilm than human-associated strains. These results evoke interactions between Ochrobactrum and the EPN symbiotic system rather than transient contamination. The main hypothesis to investigate is a toxic/antitoxic relationship because of the ability of Ochrobactrum to resist to antimicrobial and toxic compounds produced by Photorhabdus.

Successful control of a methicillin-resistant Staphylococcus aureus outbreak in a burn intensive care unit by addition of universal decolonization with intranasal mupirocin to basic infection prevention measures

BACKGROUND

Methicillin-resistant Staphylococcus aureus (MRSA) is frequently implicated in health care-associated outbreaks in burn intensive care units, incurring substantial morbidity and mortality to these high-risk patients and excess costs to health care systems.

METHODS

MRSA health care-associated infections (HAIs) were noted before and after the implementation of basic infection prevention measures and the subsequent implementation of universal decolonization with intranasal mupirocin. Pulsed-field gel electrophoresis was used to determine the relatedness of clinical isolates. A case-control study was conducted to characterize the risk factors for MRSA HAIs.

RESULTS

Basic interventions failed to decrease the rate of MRSA HAIs, although compliance with these interventions was high throughout the study. MRSA HAIs decreased from 8.53 HAIs per 1,000 patient days before the implementation of intranasal mupirocin to 3.61 HAIs per 1,000 patient days after the implementation of intranasal mupirocin (P = .033). Pulsed-field gel electrophoresis disclosed 10 unique clones with no large clusters. The case-control study revealed a significant association between MRSA HAIs and lengths of stay, body surface area burned, intubation, pressor requirement, leukocytosis, lactic acidosis, development of pneumonia, MRSA colonization, and death.

CONCLUSIONS

Basic environmental and behavioral interventions fell short of controlling a low-count, sporadic, and multiclonal MRSA outbreak in the burn intensive care unit of a tertiary medical center. However, the added implementation of universal decolonization with intranasal mupirocin was effective. Burn victims with greater disease severity were at higher risk for MRSA HAIs.

Genetic and phenotypic characterization of tetracycline-resistant Pasteurella multocida isolated from pigs

Pasteurella multocida causes single or complex respiratory disease in pigs. Although antimicrobial therapy is the most effective treatment for porcine respiratory disease, P. multocida shows increased antimicrobial resistance in Korea. Therefore, we aimed to investigate the phenotypic and genotypic characterization of tetracycline-resistant P. multocida. Thirty-seven of 454 P. multocida isolates from South Korea between 2010 and 2016 were selected. Four tet genes [tet(B) (78.4%), tet(H) (16.2%), tet(C) (5.4%), and tet(O) (2.7%)] were observed. This is the first report of tet(C) in P. multocida. Various virulence factors were observed in both tetracycline-resistant and -susceptible P. multocida isolates. Genes encoding pmHAS and pfhA were more prevalent in tetracycline-resistant than in tetracycline-susceptible isolates. Some virulence factors exhibited association with serogroups. tadD and sodA were common in serogroup A, while hsf-l was significantly associated with serogroup D (p < 0.01). Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) results showed the genetic diversity of tetracycline-resistant P. multocida. MLST showed six different sequence types (ST), with clonal complex 13 encompassing 56.8% of the strains. PFGE was more efficient in differentiating the isolates, and 29 PFGE patterns of the strains were observed. By combining these methods, identical STs and PFGE patterns were observed in isolates from different farms, suggesting that transmission of antimicrobial-resistant P. multocida strains between farms might occur in a geographically discrete population. In future, epidemiological approaches and development of effective vaccines should focus on the major clonal lineages carrying the important virulence factors and frequently observed resistance genes to prevent the transmission and control the disease.

Characterization of Listeria monocytogenes from encephalitis cases of small ruminants from different geographical regions, in Greece

AIMS

The aim of this study was to evaluate the genetic diversity and resistance phenotypes of Listeria monocytogenes strains isolated from clinical encephalitis cases, and compare this population to isolates derived from tank milk of healthy animals.

METHODS AND RESULTS

A total of 57 L. monocytogenes strains isolated from ruminant's listeriosis cases (n = 31) and from tank milk of healthy ruminants (n = 26) were characterized by species PCR, molecular serotyping, PCR detection of virulence genes, pulsed-field gel electrophoresis and antimicrobial susceptibility testing. All strains possessed inlA, inlC, inlJ, plcA, actA, hlyA and iap virulence-associated genes while serotyping analysis revealed that they were mainly assigned into IVb group. Genotyping revealed 50 pulsotypes among the 57 strains assigned into seven clusters while indistinguishable pulsotypes between clinical and milk strains were not identified. Resistance of L. monocytogenes isolates to 14-16 antimicrobial agents tested was observed and 23 antimicrobial resistance profiles (ARPs) were defined while no apparent predominant ARP type was observed among isolates.

CONCLUSIONS

Small ruminants are exposed to a broad range of antimicrobial-resistant as well as genetically diverse strains of L. monocytogenes carrying virulence-associated genes but not all of them associated with the disease. Pulsed-field gel electrophoresis analysis suggests that pulsotypes associated with encephalitis are found in farms only in association with listeriosis.

SIGNIFICANCE AND IMPACT OF THE STUDY

These findings are valuable in understanding the ecology of this important food-borne pathogen and creating awareness for the emerging antimicrobial resistance.

Salmonella Contamination in Ready-to-Eat Tilapia Sashimi Processing Plants

In this study, we investigated contamination rates and possible contamination routes of Salmonella in two typical tilapia sashimi processing plants in Taiwan. We found that the overall isolation rate was 5.0% ( n = 61), from a total of 1,218 samples collected in a year from different processing sections (freezing, scaling and bleeding, visceral removal, washing and disinfection, and packaging) and from different operating times (before processing and 3 and 6 h after processing began). In plant A, which is a relatively well-operated plant compared with plant B, Salmonella was only found in the freezing, scaling and bleeding, and visceral removal sections, with isolation rates ranging from 0 to 9.3%. No Salmonella was identified in the final ready-to-eat products at plant A. In plant B, Salmonella was found in all sections and in the final products, with isolation rates ranging from 4.6 to 36.1%. Regarding the processing times, the contamination rates increased significantly ( P < 0.05) 3 h after processing began in plant B. Among the isolates, 10 serotypes were detected, some of which are commonly observed in human salmonellosis cases in Taiwan, indicating a risk of zoonoses. However, only four isolates showed antimicrobial resistance in the current study. With molecular subtyping, we observed accumulated and persistent Salmonellae contamination patterns in plant B. These results suggest that inadequate sanitation impairs the foodborne pathogen control program in tilapia sashimi plants.

Genome Sequence Analysis of Vibrio cholerae clinical isolates from 2013 in Mexico reveals the presence of the strain responsible for the 2010 Haiti outbreak

The first week of September 2013, the National Epidemiological Surveillance System identified two cases of cholera in Mexico City. The cultures of both samples were confirmed as Vibrio cholerae serogroup O1, serotype Ogawa, biotype El Tor. Initial analyses by pulsed-field gel electrophoresis and by polymerase chain reaction-amplification of the virulence genes, suggested that both strains were similar, but different from those previously reported in Mexico. The following week, four more cases were identified in a community in the state of Hidalgo, located 121 km northeast of Mexico City. Thereafter a cholera outbreak started in the region of La Huasteca. Genomic analyses of the strains obtained in this study confirmed the presence of pathogenicity islands VPI-1 and VPI-2, VSP-1 and VSP-2, and of the integrative element SXT. The genomic structure of the 4 isolates was similar to that of V. cholerae strain 2010 EL-1786, identified during the epidemic in Haiti in 2010. This study shows that molecular epidemiology is a very powerful tool to monitor, prevent and control diseases of public health importance in Mexico.

Cross-contamination of bacteria-colonized pierced earring holes and fingers in nurses is a potential source of health care-associated infections

BACKGROUND

In recent years, the wearing of pierced earrings for personal adornment has increased among health care workers in Japan. However, the transmission dynamics between bacteria in pierced earring holes and fingers has not been clearly shown.

METHODS

Earlobes and fingers of 200 nurses (128 nurses with pierced earlobes and 72 nurses with unpierced earlobes) working at a university hospital were sampled to determine whether cross-transmission of bacteria-colonized pierced earring holes and fingers in nurse is possible.

RESULTS

Of 128 nurses who had pierced earring holes, Staphylococcus aureus was recovered from earlobes of 24 nurses (18.8%) compared with 7 of 72 nurses without pierced earring holes (9.7%) (P = .09). Of those 15 nurses yielding S aureus from both earlobes and fingers, 12 were from nurses who had pierced earring holes compared with 3 nurses without pierced earring holes. Excluding 1 nurse, antimicrobial susceptibility patterns and genotypes of S aureus from both earlobe and fingers of each nurse were identical.

CONCLUSION

Pierced earlobes can be a source of health care-associated infection via cross-transmission of bacteria from earlobe holes to fingers.

Increase in Local Protein Concentration by Field-Inversion Gel Electrophoresis

Proteins that migrate through cross-linked polyacrylamide gels (PAGs) under the influence of a constant electric field experience negative factors, such as diffusion and nonspecific trapping in the gel matrix. These negative factors reduce protein concentrations within a defined gel volume with increasing migration distance and, therefore, decrease protein recovery efficiency. Here, we describe the enhancement of protein separation efficiency for up to twofold in conventional one-dimensional PAG electrophoresis (1D PAGE), two-dimensional (2D) PAGE, and native PAGE by implementing pulses of inverted electric field during gel electrophoresis.

Genotyping of Streptococcus uberis isolates in healing process of bovine clinical mastitis

In the present work, macrorestriction analysis was applied to characterize 44 S. uberis field strains isolated from lactating cows suffering from mastitis in three dairy herds in Hesse State, Germany. Analysis of the obtained data by Pulse-Field Gel Electrophoresis (PFGE) showed that most of the isolates originating from different herds and cows were not related to each other. However, identical macrorestriction patterns were noted in 12 of 13 mastitic quarters in healing process, in three quarters even over the whole sampling period indicating persistent infection. In the present work, PFGE could detect variable levels of similarity ranging from 76 to 100%. The macrorestriction analyses revealed the presence of 10 S. uberis PFGE pattern with more than four bands difference. PFGE profiles with minor differences (only one to three bands) were considered to be subtypes. The use of sensitive genotyping methods like macrorestriction analyses by PFGE enables the differentiation among new and persistent infections. Nevertheless minor changes in macrorestriction profiles could occur which are clearly distinguishable from totally unrelated strains.

Microbiological features of indigenous typhoid cases in Taiwan and relatedness to imported cases, 2001-2014: A cross-sectional analysis

BACKGROUND

Typhoid fever was rare in Taiwan but approximately two-thirds of the cases were indigenous. The transmission source of the indigenous cases and the relatedness to the imported cases remained unknown.

METHODS

Patients with any site culture positive for Salmonella enterica serovar Typhi were identified in a teaching hospital during 2001-2014. The isolates were determined for antibiotic susceptibilities, pulsed-field gel electrophoresis (PFGE) types and single nucleotide polymorphisms (SNP) types.

RESULTS

A total of 64 typhoid episodes were identified in 63 patients. Seventeen episodes (26.6%) were imported and a majority (10, 58.8%) of them were from Indonesia. The clinical manifestations, outcomes of patients and antibiograms of isolates were similar between indigenous and imported cases. 63.3% of the isolates were ciprofloxacin-resistant. The distributions of PFGE and SNP types did not differ significantly between indigenous and imported isolates, either (P = 0.191 and 0.124, respectively). Identical PFGE pattern could be identified in indigenous isolates appearing at certain time frames, indicating outbreaks due to local transmission of certain Typhi strains.

CONCLUSIONS

The imported cases of typhoid fever from Southeast Asia were the major sources of indigenous S. Typhi infections in Taiwan. Small-scale outbreaks occurred due to local transmission of the strains after their importation.

Comparison of virulence gene profiles and genomic fingerprints of Vibrio cholerae O1 and non-O1/non-O139 isolates from diarrheal patients in southern Thailand

BACKGROUND

Vibrio cholerae is associated with severe watery diarrheal disease among people in many parts of the world, including the coastal provinces of Southern Thailand. There are relatively few studies focusing on the genetic characterization among V. cholerae isolates in this region. Therefore, this study aimed at exploring the presence of virulence genes and DNA fingerprints among V. cholerae O1 and non-O1/non-O139 isolates obtained from clinical samples in four southern coastal provinces during the period of 2001-2009 (n = 21).

RESULTS

All V. cholerae O1 isolates possessed ctxA, tcpA, zot, ace, hlyA, and vasH genes. However, only hlyA, vcsV2, and vasH genes were detected in the majority of the non-O1/non-O139 isolates. All O1 isolates showed indistinguishable PCR fingerprints by arbitrarily primed (AP)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR regardless of the geographical area and period of isolation. However, the multi-locus variable-number of tandem-repeat analysis (MLVA) could differentiate these O1 isolates (n = 11) into eight profiles. Isolates exhibiting an undistinguished MLVA profile also showed identical pulsed-field gel electrophoresis (PFGE). In addition, the O1 isolates were grouped into the same cluster by all methods used in this study.

CONCLUSIONS

This study demonstrated the presence of virulence genes and genetic diversity among different serogroups of V. cholerae isolates from clinical samples in southern Thailand. V. cholerae O1 isolated over a period of multiple years were genetically related, suggesting that they had a clonal origin, whereas non-O1/non-O139 isolates could have evolved independently.

Epidemiologic characteristics of health care-associated outbreaks and lessons learned from multiple outbreak investigations with a focus on the usefulness of routine molecular analysis

BACKGROUND

Single outbreaks have often been reported in health care settings, but the frequency of outbreaks at a hospital over time has not been described. We examined epidemiologic features of all health care-associated outbreak investigations at an academic hospital during a 5-year period.

METHODS

Health care-associated outbreak investigations at an academic hospital (2012-2016) were retrospectively reviewed through data on comprehensive hospital-wide surveillance and pulsed-field gel electrophoresis (PFGE) analysis.

RESULTS

Fifty-one health care-associated outbreaks (annual range, 8-15), including 26 (51%) outbreaks in intensive care units (ICUs), and 263 infected-colonized patients involved in these outbreaks were identified. The frequency of pathogens varied by affected location, specifically multidrug-resistant organisms (20/26 outbreaks, 77% in ICUs vs 2/25 outbreaks, 8% in non-ICUs; P < .0001) and gastroenteritis because of Clostridium difficile, norovirus, or adenovirus (1/26 outbreaks, 4% in ICUs vs 17/25 outbreaks, 68% in non-ICUs; P < .0001). Outbreaks occurred in approximately one-third of all units (37%) with some repeated instances of the same pathogens. Of 16 outbreaks caused by a bacterial pathogen evaluated by PFGE, 12 (75%) included some indistinguishable strains, suggesting person-to-person transmission or a common source.

CONCLUSIONS

This study demonstrated epidemiologic characteristics of multiple outbreaks between ICUs and non-ICUs and the value of molecular typing in understanding the epidemiology of health care-associated outbreaks.

The association of Salmonella enterica from aquatic environmental and clinical samples in Taiwan

Salmonella is one of the most common pathogens of waterborne and foodborne disease-causing pathogens. In this study, we collected 172 surface water samples from Puzih River and Kaoping River between the years 2010 and 2011. Salmonella was detected in 31.7% (32/101) and 42.2% (30/71) of the samples from the two rivers, respectively. From these positive samples, 44 Salmonella isolates were obtained from these positive samples and were characterized using serotyping and pulsed-field gel electrophoresis (PFGE) genotyping. The isolates were found with 17 serovars and 32 PFGE patterns. Salmonella enterica Newport, Bareilly, Kedougou, Albany and subspecies IIIb 50:k:z were the five most common serovars in aquatic environmental Salmonella isolates. In addition, of the total clinical samples from Chiayi and Kaohsiung, 33.7% (60/178) Newport serovars were isolated. After conducting categorical analysis, we found that the serovar Newport was not uniformly distributed cross the cities. The serovar Newport was over-represented (p<0.001) among human isolates in Chiayi and Kaohsiung. To investigate the association between Salmonella isolates from aquatic environment and human samples, we compared the environmental PFGE patterns of the test samples with those of 2438 clinical isolates, obtained from 51 hospitals across the country between 2010 and 2011. Of the 32 PFGE genotypes of environmental isolates, 8 genotypes were identical to those of clinical samples. Serovar Newport isolates with PFGE patterns SNX.119 and SNX.183 obtained from Puzih River samples were also identified in human samples at a local hospital. These suggest that there is a link between environmental and human clinical Salmonella. Identification of Salmonella serovars and genotypes present in surface water provides an indication of the specific S. enterica serovars and genotypes present in humans. This is the first study to investigate the Salmonella serovars and genotypes present in aquatic environment and humans in Taiwan.