Establishment of a universal size standard strain for use with the PulseNet standardized pulsed-field gel electrophoresis protocols: converting the national databases to the new size standard

Customizable BAC-based DNA markers for pulsed-field gel electrophoresis

DNA markers are used as a size reference and sample loading control during gel electrophoresis. Most markers are designed for conventional gel electrophoresis to separate DNA smaller than 20 kb. For larger molecules, pulsed-field gel electrophoresis (PFGE) marker is required. Limited PFGE markers are available because large DNA are prone to nicking and degradation, causing smeary bands. Here, we developed a robust marker based on bacterial artificial chromosomes (BACs) with bands up to 184 kb. This marker could consistently confer intense and distinct bands for accurate gel analysis in molecular biology studies, laboratory validations or clinical diagnosis.

Comparison of CRISPR typing and conventional molecular methods for distinguishing Laribacter hongkongensis isolates from fish, frogs and humans

High-resolution and efficient typing for Laribacter hongkongensis (L. hongkongensis) is essential for epidemiological investigation of such emerging foodborne pathogens. Clustered regularly interspaced short palindromic repeats (CRISPR) typing is an innovative molecular method that shows great promise for L. hongkongensis typing. Here, we explored the CRISPR typing method by combining CRISPR1 and CRISPR2 loci to characterize a collection of 109 L. hongkongensis isolates from humans and animals and compared it to current molecular methods such as pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). The results showed that all three methods have high discriminatory power (diversity index was 0.9902 for PFGE, 0.9663 for CRISPR and 0.9562 for MLST); strong congruence was observed between them (Rand index was 0.969 between CRISPR and PFGE, 0.953 between CRISPR and MLST, 0.958 between PFGE and MLST). CRISPR typing could well distinguish the isolates in the same STs or PFGE profiles, and the genetic information contained by the CRISPR array is useful for deep phylogenetic typing. We demonstrate that rapid CRISPR typing is a practical genetic fingerprinting tool with high resolution, comparable ease of use and lower cost, ability to track the source of various groups of L. hongkongensis strains and indication of genetic characteristics.

Genomic Characterization of a Clinical NDM-1-Producing Klebsiella michiganensis from Brazil

Public health faces daily challenges due to increasing reports of pathogenic microorganisms with new antimicrobial resistance. Klebsiella michiganensis, an emerging pathogen, poses difficulty in its identification using conventional techniques. This study presents the first documented case of NDM-1-producing K. michiganensis in Brazil, identified as the new ST418. Initially, the isolate from a tracheal secretion was misidentified as K. oxytoca. However, accurate identification was achieved through ANI analyses. Whole-genome sequencing was conducted to characterize the genetic context of the resistance genes, to identify virulence factors, and to construct a phylogenetic tree. The blaNDM-1 gene was found to be harbored on an IncFIB plasmid approximately 112 kb in length, which was transferable in conjugation assays. The detection of carbapenem resistance genes in this species highlights the importance of public health vigilance, as it may serve as a reservoir and disseminator of significant resistance genes.

Co-colonization of different species harboring KPC or NDM carbapenemase in the same host gut: insight of resistance evolution by horizontal gene transfer

Introduction

The dissemination of carbapenem-resistant Enterobacteriales (CRE) in nosocomial settings is primarily associated with the horizontal transfer of plasmids. However, limited research has focused on the in-host transferability of carbapenem resistance. In this study, ten isolates were collected from gut specimens of five individuals, each hosting two different species, including Escherichia coli, Klebsiella pneumoniae, Klebsiella aerogenes, Enterobacter cloacae, or Citrobacter koseri.

Methods

Species identification and antimicrobial susceptibility were determined by MALDI-TOF MS and broth microdilution method. Carbapenemase genes were detected and localized using PCR, S1-PFGE and southern blot. The transferability of carbapenemase genes between species was investigated through filter mating experiments, and the genetic contexts of the plasmids were analyzed using whole genome sequencing.

Results and discussion

Our results revealed that each of the ten isolates harbored a carbapenemase gene, including bla NDM-5, bla NDM-1, or bla KPC-2, on a plasmid. Five different plasmids were successfully transferred to recipient cells of E. coli, K. pneumoniae or A. baumannii by transconjugation. The genetic contexts of the carbapenemase gene were remarkably similar between the two CRE isolates from each individual. This study highlights the potential for interspecies plasmid transmission in human gut, emphasizing the colonization of CRE as a significant risk factor for the dissemination of carbapenemase genes within the host. These findings underscore the need for appropriate intestinal CRE screening and colonization prevention.

Molecular epidemiology and molecular typing methods of Acinetobacter baumannii: An updated review

The aim of this study was to go through the molecular methods used for typing of carbapenem-resistant Acientobacter baumannii (CRAB) isolates for investigating the molecular epidemiology all over the world. Multiple typing techniques are required to understand the source and nature of outbreaks caused by Acientobacter baumannii (A. baumannii) and acquired resistance to antimicrobials. Nowadays, there is gradual shift from traditional typing methods to modern molecular methods to study molecular epidemiology and infection control. Molecular typing of A. baumannii strains has been revolutionized significantly in the last 2 decades. A few sequencing-based techniques have been proven as a breakthrough and opened new prospects, which have not been achieved by the traditional methods. In this review, discussed different pre-existing and recently used typing methods to explore the molecular epidemiology of A. baumannii pertaining in context with human infections.

Multidrug Efflux System-mediated resistance in Staphylococcus aureus under a One Health approach

The aim of the study was to track the spread of antimicrobial resistance among the different sectors of One Health through the detection of Multidrug-Efflux-System in multidrug-resistant Staphylococcus aureus isolates. Multidrug-resistant (MDR) and methicillin-resistant (MRSA) S. aureus isolates were selected: 25 of human, one of animal and eight of food origin. The efflux system genes norA, norB, norC, LmrS, tet38 and msrA were screened by PCR. The activity of the efflux systems was determined by the minimum inhibitory concentration (MIC) of tetracycline and ciprofloxacin in the presence and absence of CCCP and in the quantification of ethidium bromide efflux. Furthermore, biofilm formation was determined in the presence and absence of the CCCP. The molecular epidemiology of the isolates was traced with the aid of PFGE. The gene norC was the most prevalent, detected in all isolates and msrA was the least prevalent, detected in only two isolates from humans. There was no difference in the MICs of tetracycline and ciprofloxacin in the presence of CCCP, but 55.9% of isolates showed ethidium bromide efflux. The presence of CCCP decreased the biofilm formation. Regarding the molecular epidemiology, in three clusters was a mixture of the isolates from different origins. Therefore, S. aureus MDR with active multidrug efflux systems are circulating between One Health domains and it is necessary to consider strategies to decrease this circulation in order to prevent the dissemination of resistance mediated by MES.

Characterization of ST11 and ST15 Carbapenem-Resistant Hypervirulent Klebsiella pneumoniae from Patients with Ventilator-Associated Pneumonia

Background

The prevalence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (hv-CRKP) is a serious public threat globally. Here, we performed clinical, molecular, and phenotypic monitoring of hv-CRKP strains isolated from the intensive care unit (ICU) to offer evidence for prevention and control in hospitals.

Methods

Data analysis of ICU patients suffering from ventilator-associated pneumonia (VAP) because of hv-CRKP infection, admitted at the Chinese Teaching Hospital between March 2019 and September 2021 was performed. Patients' antibiotic-resistance genes, virulence-associated genes, and capsular serotypes of these isolates were detected. Homology analysis of the strains was performed by MLST and PFGE. Six different strains were tested for their virulence traits using the serum killing test and the Galleria mellonella infection assay. For whole genome sequencing, KP3 was selected as a representative strain.

Results

Clinical data of 19 hv-CRKP-VAP patients were collected and their hv-CRKP were isolated, including 10 of ST11-KL64, 4 of ST15-KL112, 2 of ST11-KL47, 1 of ST15-KL19, 1 of ST17-KL140, and 1 of ST48-KL62. Four ST15 and 8 ST11 isolates revealed high homology, respectively. Most strains carried the carbapenemase gene blaKPC-2 (14/19, 73.68%), followed by blaOXA-232 (4/19, 21.05%). All strains were resistant to almost all the antibiotics except polymyxin and tigacycline. Ten patients were treated with polymyxin or tigacycline based on their susceptibility results, and unfortunately 6 patients died. All strains exhibited a hyper-viscous phenotype, and the majority (17/19, 89.47%) of them contained rmpA and rmpA2. The serum killing test showed that KP9 was resistant to normal healthy serum, others were intermediately or highly sensitive. G. mellonella larvae infection assay suggested that the strains in this study were hypervirulent.

Conclusion

This study highlights the dominant strain and molecular epidemiology of hv-CRKP in a hospital in China. We should pay more attention to the effect of hv-CRKP on VAP, strengthen monitoring and control transmission.

Whole-Genome Subtyping Reveals Population Structure and Host Adaptation of Salmonella Typhimurium from Wild Birds

Within-host evolution of bacterial pathogens can lead to host-associated variants of the same species or serovar. Identification and characterization of closely related variants from diverse host species are crucial to public health and host-pathogen adaptation research. However, the work remained largely underexplored at a strain level until the advent of whole-genome sequencing (WGS). Here, we performed WGS-based subtyping and analyses of Salmonella enterica serovar Typhimurium (n = 787) from different wild birds across 18 countries over a 75-year period. We revealed seven avian host-associated S. Typhimurium variants/lineages. These lineages emerged globally over short timescales and presented genetic features distinct from S. Typhimurium lineages circulating among humans and domestic animals. We further showed that, in terms of virulence, host adaptation of these variants was driven by genome degradation. Our results provide a snapshot of the population structure and genetic diversity of S. Typhimurium within avian hosts. We also demonstrate the value of WGS-based subtyping and analyses in unravelling closely related variants at the strain level.

ICESpsuAH0906, a novel optrA-carrying element conferring resistance to phenicols and oxazolidinones from Streptococcus parasuis, is transferable to Streptococcus suis

Streptococcus parasuis is a potential opportunistic zoonotic pathogen which is a close relative to Streptococcus suis, which exhibit extensive genetic exchange. The occurrence and dissemination of oxazolidinone resistance poses a severe threat to public health. However, such knowledge about the optrA gene in S. parasuis is limited. Herein, we characterized an optrA-positive multi-resistant S. parasuis isolate AH0906, in which the capsular polysaccharide locus exhibited a hybrid structure of S. suis serotype 11 and S. parasuis serotype 26. The optrA and erm(B) genes were co-located on a novel ICE of the ICESsuYZDH1 family, designated ICESpsuAH0906. IS1216E-optrA-carrying translocatable unit could be formed when excised from ICESpsuAH0906. ICESpsuAH0906 was found to be transferable from isolate AH0906 to Streptococcus suis P1/7RF at a relative high frequency of ∼ 10^-5. Nonconservative integrations of ICESpsuAH0906 into the primary site SSU0877 and secondary site SSU1797 with 2-/4-nt imperfect direct repeats in recipient P1/7RF were observed. Upon transfer, the transconjugant displayed elevated MICs of the corresponding antimicrobial agents and performed a weak fitness cost when compared with the recipient strain. To our knowledge, it is the first description of the transfer of optrA in S. prarasuis and the first report of interspecies transfer of ICE with triplet serine integrases (of the ICESsuYZDH1 family). Considering the high transmission frequency of the ICEs and the extensive genetic exchange potential of S. parasuis with other streptococci, attention should be paid to the dissemination of the optrA gene from S. parasuis to clinically more important bacterial pathogens.

Antimicrobial resistance and molecular epidemiological analysis of Escherichia fergusonii harboring the mcr gene in pigs and broiler chickens in Okinawa, Japan

The dissemination of mcr-harboring Enterobacteriaceae, e.g., Escherichia fergusonii, with resistance to colistin via animal products is a public health concern. In our previous study, E. fergusonii harboring the mcr gene were isolated from 11 pigs and 43 chickens. To understand the spread of mcr-harboring E. fergusonii in Okinawa, Japan, and to gain further insights into how they can be controlled, an antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), a conjugation test for the transferability of mcr-harboring plasmids, and PCR-based replicon typing (PBRT) were performed using the 54 strains. According to the disk-diffusion and broth microdilution methods, 9 of the 11 strains from pigs and 9 of the 43 strains from chickens had multidrug resistance (MDR). The broth microdilution method showed that all strains were resistant to colistin, and the minimum inhibitory concentration of colistin was 4-16 μg/mL. PFGE suggested identical PFGE types were being transmitted within one pig farm, within one chicken farm, and among several chicken farms. These findings showed that some mcr-harboring E. fergusonii in Okinawa exhibited MDR, and these had spread within farms and between farms. In the mcr gene conjugation test and PBRT, a type IncI2 plasmid replicon was detected in all mcr-1-harboring transconjugants. Therefore, evidence suggests that the IncI2 plasmid is probably involved in the transmission of the mcr-1 gene. It is important to monitor the antimicrobial resistance profile and dissemination of the IncI2 plasmid in mcr-harboring E. fergusonii.

Tandem Repeat of bla NDM-1 and Clonal Dissemination of a fosA3 and bla KPC-2 Co-Carrying IncR-F33: A-: B- Plasmid in Klebsiella pneumoniae Isolates Collected in a Southwest Hospital in China, 2010-2013

Introduction

Carbapenem-resistant Klebsiella pneumoniae (CRKP) has been widespread in coastal cities of eastern China since 2009. However, how CRKP spreads and evolves in southwest China is unclear.

Aim

We investigated the genetic characteristics and dissemination mechanisms of carbapenemase genes in forty-one non-repetitive CRKP isolates collected from a southwest hospital, Kunming, Yunnan, during 2010-2013.

Methodology

Drug susceptibilities were analyzed by using VITEK 2 compact system. Genetic relationships were ascertained based on multilocus sequence typing (MLST) and Pulsed-field gel electrophoresis (PFGE) analysis. Genetic backgrounds of bla _KPC-2 and bla _NDM-1 were revealed by DNA walking and high-throughput sequencing.

Results

All isolates were highly resistant to common antibiotics except for tigecycline. In total, 34 bla _KPC-2, 3 bla _NDM-1, 1 bla _IMP-4 and 3 bla _IMP-26 genes were identified and KP67 plasmid 1 co-harbored bla _NDM-1 and bla _IMP-26. Five sequence types, namely ST11, ST290, ST340, ST395 and ST437, were recognized by MLST. Surprisingly, bla _KPC-2 was only detected in ST11 strains. We described a clonal dissemination of fosA3-positive IncR-IncF33:A-:B- multireplicon plasmid carrying the gene cassettes IS26-ΔTn3-ISKpn27-bla _KPC-2-ΔISKpn6-korC-klcA-ΔrepB-Tn1721 in all ST11 isolates. Three bla _NDM-1 positive isolates belonged to three different ST types and their bla _NDM-1 genetic backgrounds were also distinct. Interestingly, the flanking regions of bla _NDM-1 in KP67 and KP72 were duplicated into one to five copies in a form of tandem repeat by the transposition of IS91 like element. The bla _NDM-1 of KP82 was carried on a common IncX3 plasmid.

Conclusion

This study described the early epidemiological characteristics of bla _KPC-2/bla _NDM-1-carrying CRKP, and reported a new tandem repeat pattern of bla _NDM-1 cluster in Yunnan. These findings extend our knowledge on the carbapenemase gene evolutions.

Genomic Insights into the Colistin Resistant mcr-Carrying Escherichia coli Strains in a Tertiary Hospital in China

Colistin is an important antimicrobial agent in the treatment of infections caused by multidrug resistant (MDR) Gram-negative bacteria. The horizontal transfer of mobile colistin resistance gene (mcr) poses a major threat to the public health worldwide. In this study, a total of thirteen mcr-carrying Escherichia coli (MCREC) strains were recovered from a tertiary hospital in Zhejiang, China, between 2016 and 2019. The minimum inhibitory concentration (MIC) of antimicrobial agents, epidemiological characteristics, and transmission dynamics of mcr-carrying isolates were analyzed using antimicrobial susceptibility testing, whole-genome sequencing, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), and southern blotting analysis. All strains were discovered to be resistant to colistin, and the majority displayed MDR phenotype. However, none of the 13 MCREC strains were resistant to carbapenems. The 13 MCREC isolates were divided into 10 different STs, including ST744, ST156, ST453, ST410, ST57, ST131, ST7034, ST2599, ST457, and ST13239, in which ST13239 was discovered for the first time. Based on core genome single nucleotide polymorphism (cgSNP) analysis, no clear epidemiological link was discovered in these strains with the exception of EC2118 and EC3807, which differ by just one SNP. A total of 35 antimicrobial resistance genes which can be divided into 14 classes were identified from the 13 MCREC isolates. According to S1-PFGE and southern blotting analyses, all 13 MCREC strains had plasmid-mediated mcr-1, and nine of them carried conjugative plasmids. In conclusion, our study revealed the emergence and dissemination of colistin-resistant E. coli isolates carrying mcr-1 in a Chinese hospital, which poses a potential risk to anti-infective therapy. More efforts should be taken to monitor the prevalence of mcr-1-carrying bacteria in China.

Laboratory surveillance of invasive Haemophilus influenzae disease in Argentina, 2011-2019

The incorporation of Haemophilus influenzae type b (Hib) vaccine into the Argentine National Immunization Program in 1998 resulted in a dramatic decrease in the incidence of invasive disease due to this serotype. We assessed 1405 H. influenzae (Hi) isolates causing invasive infections referred to the National Reference Laboratory between 2011 and 2019. Non-encapsulated Hi were the most common strains (44.5%), followed by types b (41.1%) and a (10.0%). Significant increase in the proportion of type b was observed, from 31.2% in 2011, to 50% in 2015, correlating with the peak incidence rate, later decreasing to 33.6% by 2019. We compared the genetic relationship between clones circulating during the period of increased Hib incidence (2011-2015) and those of the prevaccination-transition period (1997-1998). Four pulsotypes predominated in both periods, G, M, P and K, G being the most common. Multi-locus sequence typing revealed that the 4 pulsotypes belonged to ST6, or one of its simple or double locus variants. Isolates from fully vaccinated individuals did not differ from those of the rest of the population studied. After ruling out aspects associated with emergence of specific clones, we concluded that factors such as low booster coverage rates, delayed vaccination schedules and use of different vaccines may have contributed to the reemergence of Hib infections.

Genomic analysis of the emerging carbapenem-resistant Klebsiella pneumoniae sequence type 11 harbouring Klebsiella pneumoniae carbapenemase (KPC) in Oman

BACKGROUND AND OBJECTIVE

The presence of carbapenemase enzymes among Enterobacterales is the main mechanism to reduce susceptibility to a wide range of antibiotics. Carbapenemase enzymes such as the Klebsiella pneumoniae carbapenemase (KPC) hydrolyse beta-lactam antibiotics group, which includes carbapenem, leads to fewer treatment options. We aim to describe the first report of carbapenem-resistant K. pneumoniae (CRKP) sequence type (ST) 11 harbouring KPC in Oman.

MATERIAL AND METHODS

Five confirmed CRKP isolates were isolated from clinical samples during the period of January 2019 till December 2019. Strains were genotyped by pulse field gel electrophoresis (PFGE) for genetic relatedness. Whole genome sequencing (WGS) was performed to observe relationships with global strains using multilocus sequence typing (MLST). Antimicrobial genes, capsular loci-K-types, plasmids types and virulence genes were also identified using whole genome sequence data.

RESULTS

All five CRKP were determined to have blaKPC-2 with or without blaOX-A48 and blaNDM-2. The molecular genotyping by PFGE showed 100% similarity among the five isolates. The MLST allelic profile analysis clonally clustered our strains with SL-258, CG-11 and ST11 mainly reported from South Asia. Further molecular characterization of the capsular K-locus and O-locus genes, revealed the strains to belong to KL-47 type and OL101 type respectively. The core genome typing suggests that our strains were clonally related to Chinese strains with less than five chromosomal nucleotides differences.

CONCLUSION

Epidemiological and molecular analyses confirmed that these KPC-producing K. pneumoniae strains are from a single clone that caused multiple nosocomial infections in one health institution. This finding highlights the importance to sustain the surveillance and infection prevention efforts and to step up active screening to prevent the spread of nosocomial infection.

Genotyping of Extended Spectrum Beta-Lactamase-Producing Pseudomonas aeruginosa Isolated from People with Nosocomial Infections

Background: Pseudomonas aeruginosa nosocomial infections are among major problems associated with increased mortality and mobility among patients. Objectives: The aim of this research was to determine the molecular epidemiology of extended spectrum beta-lactamase (ESBL)-producing P. aeruginosa genotypes isolated from patients with nosocomial infections. Methods: One hundred forty-six clinical isolates of Pseudomonas spp. were obtained from a tertiary referral hospital. Phenotypic identification and PCR detection of gyrB were used to characterize P. aeruginosa. Extended spectrum beta-lactamases in samples were identified using the disk approximation test and the combination disk test (CDT). The blaSHV and blaTEM genes were detected by PCR. The strains were typed by the pulse field gel electrophoresis (PFGE), repetitive element sequence (Rep)-PCR, and enterobacterial repetitive intergenic consensus (ERIC)–PCR methods. Results: A total of 134 (91.78%) P. aeruginosa isolates were separated, 41.79% of whom were related to nosocomial infections. The extended spectrum beta-lactamase analysis test revealed that 5.97% and 66.41% of the isolates harbored the blaSHV and blaTEM genes, respectively. Enterobacterial repetitive intergenic consensus PCR, Rep-PCR, and PFGE each showed 56, 55, and 55 different patterns, respectively. Pulse-field gel electrophoresis indicated that pulso types C3 were dominant. Conclusions: The associations between ESBL production, blaSHV and blaTEM positivity, and ERIC, Rep-PCR, and PFGE patterns were not significant (P ≥ 0.05). Among nosocomial infections, a relatively high prevalence of ESBL-producing P. aeruginosa isolates was observed in the Kurdistan province of Iran. Periodic review of antibiotic resistance and molecular characterization of P. aeruginosa isolates is recommended to prevent the spread of nosocomial infections in hospitals.

Proteome-Based Serotyping of the Food-Borne Pathogens Salmonella Enterica by Label-Free Mass Spectrometry

Food-borne diseases caused by Salmonella enterica of 2500 serovars represent a serious public health problem worldwide. A quick identification for the pathogen serovars is critical for controlling food pollution and disease spreading. Here, we applied a mass spectrum-based proteomic profiling for identifying five epidemiologically important Salmonella enterica subsp. enterica serovars (Enteritidis, Typhimurium, London, Rissen and Derby) in China. By label-free analysis, the 53 most variable serovar-related peptides, which were almost all enzymes related to nucleoside phosphate and energy metabolism, were screened as potential peptide biomarkers, and based on which a C5.0 predicted model for Salmonella enterica serotyping with four predictor peptides was generated with the accuracy of 94.12%. In comparison to the classic gene patterns by PFGE analysis, the high-throughput proteomic fingerprints were also effective to determine the genotypic similarity among Salmonella enteric isolates according to each strain of proteome profiling, which is indicative of the potential breakout of food contamination. Generally, the proteomic dissection on Salmonella enteric serovars provides a novel insight and real-time monitoring of food-borne pathogens.

Prevalence and characteristics of the mcr-1 gene in retail meat samples in Zhejiang Province, China

Considering the serious threat to food safety and public health posed by pathogens with colistin resistance, colistin was banned as a growth promoter in 2017 in China. In recent years, the resistance rate of Escherichia coli isolated from animal intestines or feces to colistin has decreased. However, the prevalence and characteristics of the mcr-1 gene in retail meat have not been well explored. Herein, 106 mcr-1-negative and 16 mcr-1-positive E. coli isolates were randomly recovered from 120 retail meat samples and screened using colistin. The 106 E. coli isolates showed maximum resistance to sulfafurazole (73.58%) and tetracycline (62.26%) but susceptibility to colistin (0.00%). All 16 mcr-1-positive E. coli isolates showed resistance to colistin, were extended spectrum beta-lactamase (ESBL)-positive and exhibited complex multidrug resistance (MDR). For these 16 isolates, 17 plasmid replicons and 42 antibiotic resistance genes were identified, and at least 7 antibiotic resistance genes were found in each isolate. Acquired disinfectant resistance genes were identified in 75.00% (12/16) of the isolates. Furthermore, comparative genomic and phylogenetic analysis results indicated that these 16 mcr-1-positive E. coli isolates and the most prevalent mcr-1-harboring IncI2 plasmid in this study were closely related to other previously reported mcr-1-positive E. coli isolates and the IncI2 plasmid, respectively, showing their wide distribution. Taken together, our findings showed that retail meat products were a crucial reservoir of mcr-1 during the colistin ban period and should be continuously monitored.

Successful control of Serratia marcescens outbreak in a neonatal unit of a tertiary-care hospital in Spain

OBJECTIVE

Serratia marcescens is a Gram-negative bacterium that is found in hospital environments and commonly associated with outbreaks in neonatal units. One S. marcescens isolate was detected from a bloodstream culture from a neonate in our hospital that was followed by an outbreak. The aim of this study was to describe the molecular epidemiology of a S. marcescens outbreak in the neonatal unit.

METHODS

In order to investigate the outbreak, weekly surveillance rectal swabs were submitted for culture from all patients admitted in this unit from August to September 2018. Environmental samples were obtained from potential sources in September 2018. Typing of isolates was performed by pulsed field gel electrophoresis (PFGE). In addition, we studied the in vitro activity of chlorhexidine against S. marcescens.

RESULTS

During this period, 146 infants were hospitalised in our neonatal unit, of which 16 patients had a S. marcescens-positive sample. A total of 36 environmental surveillance samples were collected, and one sample from a stethoscope from an incubator of a colonized baby was positive for S. marcescens. All the 18 isolates, including the isolate from the stethoscope, belonged to a single PFGE cluster. We found that very low concentrations of chlorhexidine, even with application times close to 0 achieved significant reductions in the amount of S. marcescens.

CONCLUSION

A unique clone of S. marcescens caused this outbreak, including isolates from patients and from one stethoscope. The outbreak was controlled with the early implementation of specific control measures.

Isolation and characterization of Escherichia albertii originated from the broiler farms in Mississippi and Alabama

Escherichia albertii is an emerging foodborne enteropathogen with increasing outbreaks worldwide, particularly in Japan recently. However, major features of this zoonotic pathogen, such as prevalence, virulence, and antibiotic resistance (AR), still remain under characterized. In a recent pilot study, we reported isolation of E. albertii from a chicken farm in Tennessee, suggesting chicken is an important reservoir for E. albertii. In this large-scale study, we examined prevalence of E. albertii in 9 farms in Mississippi and Alabama. Of a total of 270 cloacal swabs (30 per farm), 43 were PCR positive and 12 E. albertii strains were isolated with different isolation rates in individual farms ranging from 0 to 23.3 %. Both PFGE and whole genome analysis showed the E. albertii from different farms were phylogenetically distant, but those from the same farm displayed clonal relationships. Consistently, the antibiogram, AR gene profiles, and plasmid replicon types were similar across the strains in the same farm. Notably, 9 of the 12 E. albertii strains displayed multidrug resistance; one strain was even resistant to imipenem, a clinically important carbapenem antibiotic. In addition, comparative genomics analysis showed that two chicken E. albertii clusters displayed very close evolutionary relationships and similar virulence gene profiles to human E. albertii strains. In vitro growth assay demonstrated that the anti-enterobactin antibodies could dramatically inhibit the growth of two representative chicken E. albertii, supporting the feasibility of the novel enterobactin-based immune intervention for controlling this emerging pathogen. Taken together, the findings from this study further indicated chickens as an important reservoir for E. albertii in the U.S., highlighting the need to prevent and control E. albertii in poultry production.

The Impact of Overstocking and Negative Energy Balance on Quantitative Measurement of Non-typhoidal Salmonella in Periparturient Dairy Cattle

Stressful conditions in animal production facilities may exacerbate the fecal shedding and foodborne transmission of non-typhoidal Salmonella enterica subsp. enterica. Dairy cows are reservoirs of this zoonotic microorganism, and its prevalence has roughly doubled in the past decade on dairy farms in United States. Dairy cows are commonly overstocked at the feed bunk, and stressors placed on the animal prior to parturition may exacerbate Salmonella shedding. However, no studies have evaluated the impact of overstocking and metabolic stress on fecal concentrations of the pathogen. Therefore, we conducted a field trial with 120 multiparous dairy cows randomized into one of four treatment groups with different stocking densities at the feed bunk during the periparturient period as follows: US, understocked from −60 to −1 DRC; OS, overstocked from −60 to −1 DRC; USOS, understocked from −60 to −26 DRC/overstocked from −25 to −1 DRC; and OSUS, overstocked from −60 to −26 DRC/ understocked from −25 to −1 DRC. Fecal and blood samples were collected at four time points relative to calving. qPCR assays were used to quantify Salmonella invA gene and total bacterial community from fecal samples, and a subset of isolates recovered from fecal bacterial culture were characterized using pulsed field gel electrophoresis and serotyping. Serum non-esterified fatty acids (NEFA) were measured as a metabolic stress indicator using an immunoassay. Multivariable analyses were performed to test if changes in Salmonella concentrations were associated with stocking density, energy balance, or days relative to calving. From fecal isolates, three Salmonella serovars were identified, S. Cerro; Kentucky; Meleagridis. Concentrations of Salmonella increased as cows approached calving. Higher stocking densities at the feed bunk did not impact total bacterial community or NEFA; however, cows in the overstocked groups had higher Salmonella fecal concentrations. Further, cows with higher NEFA concentrations after calving had a higher likelihood of detection of Salmonella. Future farm interventions should aim to reduce environmental and metabolic stress during the periparturient period to decrease the dissemination of Salmonella to cattle, the environment, and humans.

Colistin Resistance in Monophasic Isolates of Salmonella enterica ST34 Collected From Meat-Derived Products in Spain, With or Without CMY-2 Co-production

Colistin is a last-resort antibiotic in fighting severe infections caused by multidrug resistant Gram negative pathogens in hospitals. Zoonotic bacteria acquire colistin resistance in animal reservoirs and mediate its spread along the food chain. This is the case of non-typhoid serovars of Salmonella enterica. Colistin-resistant S. enterica in foods represents a threat to human health. Here, we assessed the prevalence of colistin-resistance in food-borne isolates of S. enterica (2014–2019; Asturias, Spain), and established the genetic basis and transferability of this resistance. Five out of 231 isolates tested (2.2%) were resistant to colistin. Four of them, belonging to the European monophasic ST34 clone of S. Typhimurium, were characterized in the present study. They were collected from pork or pork and beef meat-derived products, either in 2015 (three isolates) or 2019 (one isolate). Molecular typing with XbaI-PFGE and plasmid profiling revealed distinct patterns for each isolate, even though two of the 2015 isolates derived from the same sample. The MICs of colistin ranged from 8 to 16 mg/L. All isolates carried the mcr-1.1 gene located on conjugative plasmids of the incompatibility groups IncX4 (2015 isolates) or IncHI2 (2019 isolate). Apart from colistin resistance, the four isolates carried chromosomal genes conferring resistance to ampicillin, streptomycin, sulfonamides and tetracycline [bla_TEM–1, strA-strB, sul2, and tet(B)] and heavy metals, including copper and silver (silESRCFBAGP and pcoGE1ABCDRSE2), arsenic (arsRSD2A2BCA1D1) ± mercury (merEDACPTR), which are characteristically associated with the European ST34 monophasic clone. The 2019 isolate was also resistant to other antibiotics, comprising third generation cephalosporins and cephamycins. The latter phenotype was conferred by the bla_CMY–2 gene located on an IncI1-I(α)-ST2 plasmid. Results in the present study identified meat-derived products as a reservoir of a highly successful clone harboring transferable plasmids which confer resistance to colistin and other clinically important antibiotics. An important reduction in the number of food-borne S. enterica detected during the period of the study, together with the low frequency of colistin resistance, underlines the success of One Health initiatives, such as those implemented at the UE, to control zoonotic bacteria along the food chain and to halt the spread of antimicrobial resistance.

Occurrence and Diversity of Listeria monocytogenes Isolated from Two Pig Manure Treatment Plants in France

The presence of Listeria monocytogenes in piggery effluents intended for irrigation crops may be a source of bacterial dissemination in agriculture. The occurrence and diversity of L. monocytogenes in the farm environment were examined in two pig manure treatment systems (S1 and S2). Samples collected over the course of one year consisted of manure, the liquid fraction of treated manure (lagoon effluent), and soil surrounding the lagoon. L. monocytogenes was enumerated using the Most Probable Number (MPN) method, serotyped by PCR, genotyped by pulsed-field gel electrophoresis (PFGE), and sequenced for multilocus sequence typing (MLST). L. monocytogenes was detected in 92% of manure samples and in approximately 50% of lagoon effluent and soil samples. Concentrations ranged between 5 and 10³ MPN 100‍ ‍mL^-1. Serogroups IIa, IIb, and IVb were identified. Diversity was high with 44 PFGE profiles (252 isolates) and 17 clonal complexes (CCs) (96 isolates) with higher diversity in manure at site S1 supplied by four farms. Some PFGE profiles and CCs identified in manure or in pig feces from a previous study were also detected in lagoons and/or soil, reflecting pig L. monocytogenes circulation throughout the manure treatment and in the vicinity of the sampling sites. However, some PFGE profiles and CCs were only found in the lagoon and/or in soil, suggesting an origin other than pigs. The present study highlights the limited ability of biological treatments to eliminate L. monocytogenes from pig manure. The persistence of some PFGE profiles and CCs throughout the year in the lagoon and soil shows the ability of L. monocytogenes to survive in this type of environment.

Structural Diversity, Fitness Cost, and Stability of a BlaNDM-1-Bearing Cointegrate Plasmid in Klebsiella pneumoniae and Escherichia coli

Cointegrate/hybrid plasmids combine the genetic elements of two or more plasmids and generally carry abundant antimicrobial resistance determinants. Hence, the spread of cointegrate plasmids will accelerate the transmission of AMR genes. To evaluate the transmission risk caused by cointegrate plasmids, we investigated the structural diversity, fitness cost, and stability of a cointegrate plasmid in Klebsiella pneumoniae YZ6 and Escherichia coli EC600. The cointegrate plasmid pSL131_IncA/C_IncX3 was from a clinical Salmonella Lomita strain. After transferring the plasmid into E. coli EC600 by conjugation, we observed plasmids with different structures, including a full-length original plasmid and two truncated versions. By contrast, DNA fragment deletion and bla_CTX-M-14 gene insertion in the plasmid were detected in a transconjugant derived from K. pneumoniae YZ6. These results suggest that the structure of the plasmid was unstable during conjugation. Furthermore, both the full-length plasmid in EC600 and the structurally reorganized plasmid in YZ6 imposed a fitness cost on the bacterial host and enhanced biofilm formation ability. Serial passaging in antibiotic-free medium resulted in a rapid decline of the plasmid in YZ6. However, the stability of the structurally reorganized plasmid in YZ6 was improved via serial passaging in antibiotic-containing medium. SNP calling revealed that mutations of the outer membrane porin may play an essential role in this process. These findings indicate that structural versatility could contribute to the dissemination of cointegrate plasmids. Although the plasmid incurred a fitness cost in other Enterobacteriaceae species, positive selection could alleviate the adverse effects.

Use of high-dose ciprofloxacin for recurrent biofilm-forming multidrug-resistant Klebsiella pneumoniae bacteremia

Introduction

Klebsiella pneumoniae is a significant nosocomial pathogen. We aimed to assess the clinical success following high-dose ciprofloxacin for recurrent bacteremia from biofilm-forming multidrug resistant Klebsiella pneumoniae in a liver transplanted patient.

Case report

A 55-year-old male had undergone liver transplantation and at day 10 he developed fever and dysuria. Two blood cultures became positive and were identified by Vitek2 (BioMérieux, USA) as K. pneumoniae. From his urine K. pneumoniae was isolated. Based on antimicrobial susceptibility (AST) panel (Vitek2), i.v. meropenem 1 g 8 hourly and i.v. amikacin 15 mg/kg/ daily (5 days) were started (the isolate was ciprofloxacin-resistant). Following 14 days of meropenem he was discharged and 3 days later he was readmitted with fever and dysuria. Since the blood and urine isolate was K. pneumoniae, based on AST 21 days of meropenem were given, the patient was discharged and 3 days later he was readmitted with fever and dysuria. Since this was the 3^rd episode with K. pneumoniae bacteremia, to exclude the focus of infection contrast-enhanced computed tomography and ¹⁸F-fluorodeoxyglucose-positron emission tomography were done but both were normal.Based on multilocus sequence typing (MLST) and microtiter plate assay, biofilm forming magA(K1)-positive (+) K. pneumoniae CC23 was found. The patient was having continuous asymptomatic bacteriuria with similar (magA(K1)-positive (+) K. pneumoniae CC23) isolate; we opted for high dose oral ciprofloxacin (800 mg, 8 hourly) for 7 days.

Conclusions

Following a high dose of oral ciprofloxacin, we were able to achieve urinary microbial clearance and a permanent cure following (magA(K1)-positive (+) K. pneumoniae CC23) bacteremia. This could be a promising therapy to achieve microbial clearance from biofilm-forming multidrug-resistant K. pneumoniae.

Emergence of a KPC Variant Conferring Resistance to Ceftazidime-Avibactam in a Widespread ST11 Carbapenem-Resistant Klebsiella pneumoniae Clone in China

Carbapenem-resistant Klebsiella pneumoniae (CRKP) infection poses a great threat to public health worldwide, and KPC-2-producing strains are the main factors responsible for resistance to carbapenems in China. Ceftazidime/avibactam (CZA) is a novel β-lactam/β-lactamase inhibitor combination with good activity against KPC-2 carbapenemase and is becoming the most important option for treating KPC-producing CRKP infection. Here, we report the emergence of a novel KPC-2 variant, designated KPC-74, produced by K. pneumoniae strain KP55, that conferred CZA resistance in a patient after CZA exposure. The novel bla_KPC–74 variant showed a deletion of 6 nucleotides at positions 712–717 compared with bla_KPC–2, and this deletion resulted in the consequent deletion of glycine and valine at positions 239 and 240. Antimicrobial susceptibility testing showed that KP55 presents multidrug resistance, including resistance to CZA and ertapenem, but is susceptible to imipenem, meropenem, and colistin. The bla_KPC–74 gene was located on a plasmid, as determined by S1-nuclease pulsed-field gel electrophoresis followed by southern blotting, and confirmed to be 133,766 bp in length by whole-genome sequencing on both the Illumina and MinION platforms. The CZA resistance phenotype of the novel KPC variant was confirmed by both transformation of the bla_KPC–74-harboring plasmid and a bla_KPC–74 gene cloning assay, showing a 64-fold higher CZA minimum inhibitory concentration (MIC) than the recipient strains. The G239_V240del observed in KPC-74 was outside the omega-loop region but was still close to the active site Ser70 and omega-loop in the protein tertiary structure. The enzyme kinetic parameters and IC₅₀ values further indicated that the hydrolytic activity of the KPC-74 enzyme against ceftazidime was potentiated twofold and that the affinity between KPC-74 and avibactam was alleviated 17-fold compared with that of the KPC-2 allele. This CZA resistance mediated by KPC-74 could be selected after CZA therapy and evolved to be more diverse and heterogeneous. Surveillance of CZA resistance is urgently needed in clinical settings.

High rates of Salmonella contamination in raw kibbe from commercial establishments: predominance of Salmonella Give

Salmonella is one of the major causes of gastroenteritis worldwide in both humans and animals and one of the main agents involved in foodborne disease outbreaks. In this study, 70 raw kibbe samples from different commercial establishments were analyzed for Salmonella spp. The isolates were seroyped and tested for susceptibility to antimicrobial agents. Pulsed-field Gel Electrophoresis was carried out following the standard protocol of the PulseNet network. Fifteen (21.4%) samples were contaminated with Salmonella and S. Give was the prevalent serotype (46.7%). Similarity of 96.3% was observed among the S. Give isolates (n = 7), which indicates the possible spread of the same clone in the analyzed commercial establishments. S. Rissen and S. Typhimurium showed antimicrobial resistance. The detection of a significant percentage of contamination in raw kibbe and of the resistant strains indicates the risk that the consumption of this dish may represent.

Free-Living Aquatic Turtles as Sentinels of Salmonella spp. for Water Bodies

Reptile-associated human salmonellosis cases have increased recently in the United States. It is not uncommon to find healthy chelonians shedding Salmonella enterica. The rate and frequency of bacterial shedding are not fully understood, and most studies have focused on captive vs. free-living chelonians and often in relation to an outbreak. Their ecology and significance as sentinels are important to understanding Salmonella transmission. In 2012-2013, Salmonella prevalence was determined for free-living aquatic turtles in man-made ponds in Clarke and Oconee Counties, in northern Georgia (USA) and the correlation between species, basking ecology, demographics (age/sex), season, or landcover with prevalence was assessed. The genetic relatedness between turtle and archived, human isolates, as well as, other archived animal and water isolates reported from this study area was examined. Salmonella was isolated from 45 of 194 turtles (23.2%, range 14-100%) across six species. Prevalence was higher in juveniles (36%) than adults (20%), higher in females (33%) than males (18%), and higher in bottom-dwelling species (31%; common and loggerhead musk turtles, common snapping turtles) than basking species (15%; sliders, painted turtles). Salmonella prevalence decreased as forest cover, canopy cover, and distance from roads increased. Prevalence was also higher in low-density, residential areas that have 20-49% impervious surface. A total of 9 different serovars of two subspecies were isolated including 3 S. enterica subsp. arizonae and 44 S. enterica subsp. enterica (two turtles had two serotypes isolated from each). Among the S. enterica serovars, Montevideo (n = 13) and Rubislaw (n = 11) were predominant. Salmonella serovars Muenchen, Newport, Mississippi, Inverness, Brazil, and Paratyphi B. var L(+) tartrate positive (Java) were also isolated. Importantly, 85% of the turtle isolates matched pulsed-field gel electrophoresis patterns of human isolates, including those reported from Georgia. Collectively, these results suggest that turtles accumulate Salmonella present in water bodies, and they may be effective sentinels of environmental contamination. Ultimately, the Salmonella prevalence rates in wild aquatic turtles, especially those strains shared with humans, highlight a significant public health concern.

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.

Successful control of Serratia marcescens outbreak in a neonatal unit of a tertiary-care hospital in Spain

OBJECTIVE

Serratia marcescens is a Gram-negative bacterium that is found in hospital environments and commonly associated with outbreaks in neonatal units. One S. marcescens isolate was detected from a bloodstream culture from a neonate in our hospital that was followed by an outbreak. The aim of this study was to describe the molecular epidemiology of a S. marcescens outbreak in the neonatal unit.

METHODS

In order to investigate the outbreak, weekly surveillance rectal swabs were submitted for culture from all patients admitted in this unit from August to September 2018. Environmental samples were obtained from potential sources in September 2018. Typing of isolates was performed by pulsed field gel electrophoresis (PFGE). In addition, we studied the in vitro activity of chlorhexidine against S. marcescens.

RESULTS

During this period, 146 infants were hospitalised in our neonatal unit, of which 16 patients had a S. marcescens-positive sample. A total of 36 environmental surveillance samples were collected, and one sample from a stethoscope from an incubator of a colonized baby was positive for S. marcescens. All the 18 isolates, including the isolate from the stethoscope, belonged to a single PFGE cluster. We found that very low concentrations of chlorhexidine, even with application times close to 0 achieved significant reductions in the amount of S. marcescens.

CONCLUSION

A unique clone of S. marcescens caused this outbreak, including isolates from patients and from one stethoscope. The outbreak was controlled with the early implementation of specific control measures.

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.

Temporal Trend of ST131 Clone among Urinary Escherichia coli Isolates in the Community: A Taiwan National Surveillance from 2002 to 2016

Sequence type (ST) 131 is a multidrug-resistant pandemic lineage of E. coli responsible for extraintestinal infections. Few surveillance data of ST131 included all antimicrobial-susceptible and -resistant isolates or focused on community-acquired urinary tract infection (UTI). From a population-based surveillance pool of 2997 outpatient urine E. coli isolates, 542 were selected for detection of ST131 based on ciprofloxacin and/or cefotaxime resistance. Pulsed-field gel electrophoresis (PFGE) was performed on all ST131 isolates to further determine their relatedness. The estimated overall ST131 prevalence in this community UTI cohort increased from 11.2% (in 2002-2004), 12.2% (in 2006-2008), 13.6% (in 2010-2012), to 17.4% in 2014-2016 (p < 0.01). In the ciprofloxacin-resistant/cefotaxime-resistant group, ST131 increased from 33.3% in 2002-2004 to 72.1% in 2014-2016 (p < 0.01). In the ciprofloxacin-resistant/cefotaxime-susceptible group, ST131 was found in 24.3% overall without significant increase in its prevalence over time. PFGE showed emergence of a cluster of ciprofloxacin-resistant/cefotaxime-resistant ST131 carrying Gr. 1 CTX-M ESBL in 2014-2016, especially 2016. Multivariate analysis revealed that age (≥65 y.o) and ciprofloxacin resistance were independent factors associated with ST131. This longitudinal surveillance showed that ciprofloxacin-resistant/cefotaxime-susceptible ST131 has been circulating in the community since 2002 but ciprofloxacin-resistant/cefotaxime-resistant ST131 increased rapidly in the later years.

Analysis of blaCHDL Genes and Insertion Sequences Related to Carbapenem Resistance in Acinetobacter baumannii Clinical Strains Isolated in Warsaw, Poland

Acinetobacter baumannii is an important cause of nosocomial infections worldwide. The elucidation of the carbapenem resistance mechanisms of hospital strains is necessary for the effective treatment and prevention of resistance gene transmission. The main mechanism of carbapenem resistance in A. baumannii is carbapenemases, whose expressions are affected by the presence of insertion sequences (ISs) upstream of bla_CHDL genes. In this study, 61 imipenem-nonsusceptible A. baumannii isolates were characterized using phenotypic (drug-susceptibility profile using CarbaAcineto NP) and molecular methods. Pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) methods were utilized for the genotyping. The majority of isolates (59/61) carried one of the following acquired bla_CHDL genes: bla_OXA-24-like (39/59), ISAba1-bla_OXA-23-like (14/59) or ISAba3-bla_OXA-58-like (6/59). Whole genome sequence analysis of 15 selected isolates identified the following intrinsic bla_OXA-66 (OXA-51-like; n = 15) and acquired class D β-lactamases (CHDLs): ISAba1-bla_OXA-23 (OXA-23-like; n = 7), ISAba3-bla_OXA-58-ISAba3 (OXA-58-like; n = 2) and bla_OXA-72 (OXA-24-like; n = 6). The isolates were classified into 21 pulsotypes using PFGE, and the representative 15 isolates were found to belong to sequence type ST2 of the Pasteur MLST scheme from the global IC2 clone. The Oxford MLST scheme revealed the diversity among these studied isolates, and identified five sequence types (ST195, ST208, ST208/ST1806, ST348 and ST425). CHDL-type carbapenemases and insertion elements upstream of the bla_CHDL genes were found to be widespread among Polish A. baumannii clinical isolates, and this contributed to their carbapenem resistance.

Clonal spread of multi-resistant Gallibacterium anatis isolates among Iranian broilers and layers

Gallibacterium anatis is a common cause of reproductive tract infection in chickens, which leads to reduced egg production and increased mortality. This study was undertaken to investigate prevalence of G. anatis in 12 poultry flocks originating from Iranian provinces with leading chicken production and to determine genetic diversity, antimicrobial resistance, and the presence of major antigens of the isolates investigated. Out of the 120 chicken tracheal samples collected and tested, 84 (70%) were positive for G. anatis. Genotyping by Pulse Field Gel Electrophoresis and genome sequencing revealed a total of 24 pulsotypes for 71 strains (at a 87% similarity level) and seven genome clusters comprising 21 strains (97% similarity level), respectively. The combination of the two typing methods confirmed the presence of several genotypes originating from a common ancestor affecting poultry yet also suggested that identical clones were shared among chickens within farms and between different farms. The latter finding is to our knowledge the first example of clonal presence of G. anatis in epidemiologically unrelated farms. The 21 sequenced strains were characterized against a panel of commonly used antibiotics and showed lowered sensitivity to tetracycline (76.2%) and enrofloxacin (90.5%). The widespread presence of multiresistant G. anatis isolates calls for non-antibiotic prophylactics. Three major immunogen genes, gtxA, Gab_1309 and Gab_2312 were detected in the isolates indicating these antigens likely represent effective vaccine targets. A conserved sequence of the gtxA gene across a range of epidemiologically independent strains suggests the use of GtxA for future vaccine development purposes.

Molecular Characterization of Cephalosporin-Resistant Salmonella Enteritidis ST11 Isolates Carrying blaCTX-M from Children with Diarrhea

Salmonella Enteritidis is an important foodborne pathogen with high prevalence of resistance to cephalosporins, imposing a serious threat to public health. Therefore, a total of 162 Salmonella Enteritidis isolates collected from child patients in China from 2007 to 2017 were characterized for their resistance to cephalosporins and investigated the transmission characteristics of cephalosporin resistance gene. We found that 15 (9.26%) isolates were all resistant to cefalotin (minimum inhibitory concentration [MIC] ≥512 μg/mL), ceftazidime (MIC 16-128 μg/mL), ceftriaxone (MIC 64 to ≥512 μg/mL), ceftiofur (MIC 64-256 μg/mL), and cefotaxime (MIC 64 to ≥512 μg/mL) with the possession of cephalosporin resistance genes bla_CTX-M-55 (n = 13), bla_CTX-M-101 (n = 1), and bla_CTX-M-153 (n = 1). Molecular typing further revealed that these 15 isolates belonged to sequence type ST11 and shared close pulsed-field gel electrophoresis patterns, suggesting the possibility of clonal spread in Salmonella Enteritidis interspecies. Furthermore, conjugation experiments were successfully performed in 13 of 15 isolates, and bla_CTX-M-55 was present on conjugative plasmids with sizes ranging from 54.7 to 173.4 kb. Compared with recipient Escherichia coli C600, transconjugants conferred elevated MICs for cephalosporins ranging from 2- to 2048-fold. The genetic structure surrounding of bla_CTX-M-55 gene in transconjugants were ΔISEcp1-bla_CTX-M-55-orf477 (n = 8) and ISEcp1-bla_CTX-M-55-orf477 (n = 3), respectively. Taken together, bla_CTX-M on the plasmids might contribute to cephalosporin resistance in Salmonella Enteritidis, and conjugative transfer of bla_CTX-M-55 might facilitate the spread of cephalosporin resistance in Salmonella Enteritidis. Hence, effective mitigation measurements are needed to reduce the threat caused by cephalosporin-resistant Salmonella Enteritidis to public health.

Pulsed-Field Gel Electrophoresis (PFGE) Analysis of Listeria monocytogenes

PFGE is a valuable tool for assessing L. monocytogenes strain interrelatedness. It is based on the study of total bacterial DNA restriction patterns. Cells are embedded in agarose plugs before being lysed. The released DNA is then digested into large fragments by restriction enzymes. As DNA fragments are too large to be separated by traditional electrophoresis in an agarose gel, changes in the direction of the electrical current are periodically applied in order to allow the proper migration of large DNA fragments. Strains are characterized by the obtained DNA fragment patterns or pulsotypes which vary depending on the number and size of bands.

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

Pooled Plasmid Sequencing Reveals the Relationship Between Mobile Genetic Elements and Antimicrobial Resistance Genes in Clinically Isolated Klebsiella pneumoniae

Plasmids remain important microbial components mediating the horizontal gene transfer (HGT) and dissemination of antimicrobial resistance. To systematically explore the relationship between mobile genetic elements (MGEs) and antimicrobial resistance genes (ARGs), a novel strategy using single-molecule real-time (SMRT) sequencing was developed. This approach was applied to pooled conjugative plasmids from clinically isolated multidrug-resistant (MDR) Klebsiella pneumoniae from a tertiary referral hospital over a 9-month period. The conjugative plasmid pool was obtained from transconjugants that acquired antimicrobial resistance after plasmid conjugation with 53 clinical isolates. The plasmid pool was then subjected to SMRT sequencing, and 82 assembled plasmid fragments were obtained. In total, 124 ARGs (responsible for resistance to β-lactam, fluoroquinolone, and aminoglycoside, among others) and 317 MGEs [including transposons (Tns), insertion sequences (ISs), and integrons] were derived from these fragments. Most of these ARGs were linked to MGEs, allowing for the establishment of a relationship network between MGEs and/or ARGs that can be used to describe the dissemination of resistance by mobile elements. Key elements involved in resistance transposition were identified, including IS26, Tn3, IS903B, ISEcp1, and ISKpn19. As the most predominant IS in the network, a typical IS26-mediated multicopy composite transposition event was illustrated by tracing its flanking 8-bp target site duplications (TSDs). The landscape of the pooled plasmid sequences highlights the diversity and complexity of the relationship between MGEs and ARGs, underpinning the clinical value of dominant HGT profiles.

Research Note: Identification and characterization of Salmonella spp. in mechanically deboned chickens using pulsed-field gel electrophoresis

Salmonella is one of the common foodborne bacteria, causing 80.3 million illnesses every year worldwide. This study was conducted to isolate and identify Salmonella enterica serovars from poultry samples responsible for causing foodborne poisoning in the Mississippi area, United States. A total of 55 S. enterica serovars—Enteritidis (6), Oranienburg (1), Schwarzengrund (8), Heidelberg (4), Kentucky (22), 4, [5], 12:i:- (1), Montevideo (2), Infantis (9), and multi serotypes (2)—were isolated from approximately 110 poultry samples. Through pulsed-field gel electrophoresis (PFGE) analysis, 8 to 13 bands were obtained. The profiles showed >90% similarity in strains within the same type. Consequently, PFGE could be a useful tool to determine chromosomal similarity (clonality of strains) that can be used to trace down epidemiologic sources and geographical origins of Salmonella.

Histopathological and microbiological study of porcine lymphadenitis: contributions to diagnosis and control of the disease

Tuberculosis like lesions (TBL) in free-range pigs are characterised by presenting a marked heterogeneity in pathology and microbiology features, with a notorious role of Mycobacterium tuberculosis complex (MTC), Trueperella pyogenes and different Streptococcus species. However, the capacity of these microorganism to spread to different organic cavities leading to a generalised disease is unknown. Therefore, this study evaluated the organic distribution of these agents in free-range pig carcasses whole condemned due to generalised TBL.

A total of 37 totally condemned animals were analysed, and samples of lymph nodes and organs were obtained (n = 262) and subjected to histopathological and microbiological examination. In addition, T. pyogenes and streptococci species were further characterised by PFGE analysis. Two different patterns were evidenced with lack or occasional lesions in superficial inguinal (SILN) and popliteal (PLN) lymph nodes and advanced lesions in submandibular (SLN) (35/36) and gastrohepatic (GHLN) (33/35) lymph nodes (stages III and IV). Early stage granulomas (stage I and II) prevailed in lungs (16/20), liver (14/31) and spleen (7/18). The microbiological analysis revealed that MTC, detected by qPCR, was present in 31 out of 37 animals and 90 (90/262) samples. In 26 out of the 31 pigs, MTC was detected from two or more organs. SLN (24/31) and GHLN (19/31) were the MTC⁺ organs most frequently detected, with 29 out of 31 MTC⁺ pigs detected as positive in one or both samples, which points out that both lymph nodes must be included in the sampling of surveillance programs. Other pathogens, such as T. pyogenes and Streptococcus spp., were also involved in generalised lymphadenitis, being frequently isolated from SLN and other organs, such as liver (T. pyogenes), tonsils or lung (Streptococcus spp.). A wide genetic diversity among streptococci was observed, showing the ubiquitous character of these pathogens, however, the isolation of a single clone of T. pyogenes from different organic locations from animals with generalised TBL was a common finding of this study, highlighting that the role of this pathogen in porcine lymphadenitis may be underestimated. These results should be considered in future studies on the pathogenesis and control of porcine lymphadenitis.

Characterization of blaKPC-2-Harboring Klebsiella pneumoniae Isolates and Mobile Genetic Elements from Outbreaks in a Hospital in Ecuador

Aim: To investigate the mobile genetic elements harboring bla_KPC gene in carbapenem-resistant Klebsiella pneumoniae recovered during a 6-month outbreak in a high-complexity hospital from Ecuador. Results: A total of 62 isolates belonging to ST258 pilv-I-positive (n = 45), ST25 serotype K2 (n = 8), ST348 (n = 6), ST42 (n = 1), ST196 (n = 1), and ST1758 (n = 1) were collected from intensive care unit (ICU), neurosurgery, burn unit, internal medicine, pneumology, and neurology. Pulsed-field gel electrophoresis analysis showed two major clusters of ST258 and ST25 related to bloodstream infections and pneumonia circulating in ICU. The PCR assay showed that in non-ST258 isolates, the bla_KPC-2 gene were located on the Tn4401a transposon inserted in the transferable pKpQIL-like IncFII_K2 plasmid; the whole-genome sequencing of ST258 clone showed two plasmids, the bla_KPC-2 gene was located on nonconjugative IncR plasmid, whereas the IncFIB/IncFII plasmid lacked ß-lactamase genes. We found an IncM plasmid in bla_KPC-2-harboring Klebsiella pneumoniae ST1758 clone. Conclusions: These findings highlight the presence of pKpQIL-like plasmids in non-ST258 and nonconjugative plasmids in ST258 isolates causing hospital outbreaks.

Plasmid-borne colistin resistance gene mcr-1 in a multidrug resistant Salmonella enterica serovar Typhimurium isolate from an infant with acute diarrhea in China

BACKGROUND

Antimicrobial resistance of Salmonella enterica is a major global concern. Recent findings suggest that colistin as a last resort treatment for multidrug-resistant gram-negative bacteria is seriously threatened by the report of plasmid-mediated colistin resistance gene mcr-1 in China.

METHODS

A total of 827 S. Typhimurium isolates were recovered from 4 cities of China, including Henan, Shanghai, Zhejiang, and Hubei provinces. Subsequently, mcr-1 presence was identified by PCR screening. Antimicrobial susceptibility testing was performed by broth microdilution using a 96-well microtiter plate. Plasmid conjugation transfer experiments were conducted using Escherichia coli J53 as the recipient.

RESULTS

Only one mcr-1 positive strain from the stool sample of an infant with acute diarrhea was isolated. Apart from colistin, the mcr-1-positive isolate showed co-resistance to the third-generation cephalosporins, ampicillin, nalidixic acid, tetracycline, chloramphenicol, sulfisoxazole, gentamicin, and cefotaxime revealing a multidrug-resistant phenotype. This strain harbored mcr-1 on a 227 kb IncHI2 plasmid, termed pJZ26, which could be transferred to E. coli J53. In addition to mcr-1, pJZ26 coharbored other resistance genes, including aph(4)-Ia, aac(3)-IVa, fosA, floR, sul2, and bla_CTX-M-14. Compared with p2474-MCR1 and pHYEC7-IncHI2, pJZ26 contains an additional 4.6 kb fragment harboring the resistance gene tet(A) and its regulator tetR located on TnAs1 transposable element, which could mediate resistance to tetracycline.

CONCLUSIONS

These findings highlight that the fact the mcr-1-harboring plasmid pJZ26 has a high potential to disseminate the mcr-1 gene and further challenge the clinical treatment.

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.

Molecular characterization of clinical and environmental Vibrio parahaemolyticus isolates in Huzhou, China

Vibrio parahaemolyticus is responsible for seafood-borne gastroenteritis worldwide. Isolates of V. parahaemolyticus from clinical samples (n = 54) and environmental samples (n = 38) in Huzhou were analyzed by serological typing, virulence gene detection, antibiotic resistance testing, and pulsed-field gel electrophoresis (PFGE) for molecular typing. O3:K6 was the main serotype and tlh+tdh+trh- was the most frequently detected virulence genotype in clinical strains. O2:Kut was the main serotype and tlh+tdh-trh- was the most frequently detected virulence genotype in environmental strains. Antibiotic resistance testing indicated that the isolates were highly resistant to ampicillin (90.76%), followed by gentamicin and tetracycline. Following the restriction enzyme NotI digestion, the 91 strains yielded 81 PFGE patterns, and 16 clones had similarity values of > 85.00%, indicating a high level of diversity. Finally, there may be cross-contamination between freshwater and seawater products, so it is necessary to strengthen supervision of food processing.

Evaluation of lactic acid bacteria strains isolated from fructose-rich environments for their mannitol-production and milk-gelation abilities

Mannitol is a sugar alcohol, or polyol, widely used in the food industry because of its low-calorie properties. Industrial production of mannitol is difficult and expensive. However, certain bacterial species are known to produce mannitol naturally, including certain lactic acid bacteria and fructophilic lactic acid bacteria (LAB). In this study, bacterial strains isolated from fructose-rich sources, including flowers, leaves, and honey, were identified by 16S rRNA sequence analysis as Leuconostoc, Fructobacillus, Lactococcus, and Lactobacillus species and 4 non-LAB species. DNA profiles generated by pulsed-field gel electrophoresis discriminated 32 strains of Leuconostoc mesenteroides and 6 Fructobacillus strains. Out of 41 LAB strains isolated, 32 were shown to harbor the mdh gene, which encodes the mannitol dehydrogenase enzyme, and several showed remarkable fructose tolerance even at 50% fructose concentrations, indicating their fructophilic nature. Several of the strains isolated, including Leuconostoc mesenteroides strains DPC 7232 and DPC 7261, Fructobacillus fructosus DPC 7237, and Fructobacillus fructosus DPC 7238, produced higher mannitol concentrations than did the positive control strain Limosilactobacillus reuteri DSM 20016 during an enzymatic screening assay. Mannitol concentrations were also examined via HPLC in 1% fructose de Man, Rogosa, and Sharpe medium (FMRS) or 1% fructose milk (FM). Among the strains, Fructobacillus fructosus DPC 7238 displayed high fructose utilization (9.27 g/L), high mannitol yield (0.99 g of mannitol/g of fructose), and greatest volumetric productivities (0.46 g/L per h) in FMRS. However, Leuconostoc mesenteroides DPC 7261 demonstrated the highest fructose utilization (8.99 g/L), mannitol yield (0.72 g of mannitol/g of fructose), and volumetric productivities (0.04 g/L per h) in FM. Storage modulus G' (>0.1 Pa) indicated a shorter gelation time for Limosilactobacillus reuteri DSM 20016 (8.73 h), followed by F. fructosus DPC 7238 (11.57 h) and L. mesenteroides DPC 7261 (14.52 h). Our results show that fructose-rich niches can be considered important sources of fructophilic LAB strains, with the potential to be used as starter cultures or adjunct cultures for the manufacture of mannitol-enriched fermented dairy products and beverages.

Coexistence of blaKPC-2-IncN and mcr-1-IncX4 plasmids in a ST48 Escherichia coli strain in China

OBJECTIVES

The aim of this study was to explore the genomic content of a bla_KPC-2- and mcr-1-harbouring Escherichia coli strain and to clarify the molecular mechanism for the transmission of multidrug resistance.

METHODS

Antimicrobial susceptibility testing was conducted by the broth microdilution method to determine the resistance profile. Filter-mating conjugation assays were performed to confirm the plasmid transfer ability. Whole-genome sequence data were acquired by a combination of Illumina paired-end reads and Nanopore long-read sequencing.

RESULTS

Escherichia coli strain QE11-421 was an mcr-1-positive colistin-resistant isolate that co-harboured the bla_KPC-2 gene conferring carbapenem resistance. Genome sequence data confirmed QE11-421 as a sequence type 48 (ST48) E. coli that harboured five large conjugative plasmids encoding several multidrug resistance genes. The bla_KPC-2 gene was located on a Tn3-Tn4401 composite transposon, which is part of a 65-kb multidrug-resistant IncN plasmid. The mcr-1 gene was harboured on another 33-kb IncX4 plasmid that was more conserved and presented few antimicrobial resistance determinants. No copies of insertion sequence ISApl1 were found flanking the mcr-1 gene, decreasing the mobility of mcr-1 based on its original Tn6330 transposon.

CONCLUSIONS

Horizontal transfer of multidrug resistance plasmids or resistance-related transposon units was responsible for the emergence of this notorious superbug. The coexistence of bla_KPC-2-IncN and mcr-1-IncX4 plasmids in a ST48 E. coli strain in humans poses a great threat.

Prevalence and antimicrobial-resistance profiles of Salmonella spp. isolated from green anoles (Anolis carolinensis) collected on the Haha-jima of the Ogasawara archipelago, Japan

We investigated the prevalence of Salmonellaenterica and its antimicrobial resistance from 79 green anoles, the invasive alien species inhabits Haha-jima of the Ogasawara archipelago. Samples were collected during the period between 2009 and 2010. The resistance of S. enterica of these samples against 12 common antimicrobial agents was also determined. Salmonella strains, including serovar Oranienburg and Aberdeen, were detected from the large intestines of 30.4% of 79 green anole samples. And 37.5% of which were resistant to Oxytetracycline. This study suggests that green anoles may play an important role of the infection of S. enterica on this island. Attention is needed from the aspect of public and ecological health.