Characterisation of Bordetella bronchiseptica isolated from rabbits in Fujian, China

Bordetella bronchiseptica is a potential zoonotic pathogen, which mainly causes respiratory diseases in humans and a variety of animal species. B. bronchiseptica is one of the important pathogens isolated from rabbits in Fujian Province. However, the knowledge of the epidemiology and characteristics of the B. bronchiseptica in rabbits in Fujian Province is largely unknown. In this study, 219 B. bronchiseptica isolates recovered from lung samples of dead rabbits with respiratory diseases in Fujian Province were characterised by multi-locus sequencing typing, screening virulence genes and testing antimicrobial susceptibility. The results showed that the 219 isolates were typed into 11 sequence types (STs) including five known STs (ST6, ST10, ST12, ST14 and ST33) and six new STs (ST88, ST89, ST90, ST91, ST92 and ST93) and the ST33 (30.14%, 66/219), ST14 (26.94%, 59/219) and ST12 (16.44%, 36/219) were the three most prevalent STs. Surprisingly, all the 219 isolates carried the five virulence genes (fhaB, prn, cyaA, dnt and bteA) in the polymerase chain reaction screening. Moreover, the isolates were resistant to cefixime, ceftizoxime, cefatriaxone and ampicillin at rates of 33.33%, 31.05%, 11.87% and 3.20%, respectively. This study showed the genetic diversity of B. bronchiseptica in rabbits in Fujian Province, and the colonisation of the human-associated ST12 strain in rabbits in Fujian Province. The results might be useful for monitoring the epidemic strains, developing preventive methods and preventing the transmission of epidemic strains from rabbits to humans.

Molecular characteristics and antibiotic susceptibility profiles of Mycoplasma bovis associated with mastitis on dairy farms in China

Mycoplasma bovis (M. bovis) is regarded as the most prevalent mycoplasma species causing bovine mastitis worldwide. This study was conducted with the objectives to: (1) estimate M. bovis prevalence in samples from clinical mastitis and bulk tank milk; (2) assess genetic diversity and population structure of isolates; and (3) determine antibiotic susceptibility of isolates to nine antimicrobials. Milk samples (n = 476), including 450 clinical mastitis and 26 bulk tank milk samples from 23 farms (each with >1000 lactating cows) in 10 provinces of China were collected between May 2018 and September 2019. M. bovis cultured from milk samples were analyzed by multi-locus sequence typing. Minimum inhibitory concentrations of all isolates to nine antimicrobials were determined. Differences in minimum inhibitory concentration values were assessed by Kruskal-Wallis test with Bonferroni correction. The positive proportions of M. bovis in clinical mastitis samples and bulk tank milk samples were 39/450 (8.7%) and 11/26 (42.3%), respectively. Based on multi-locus sequence typing, the 50 isolates were identified as three sequence types, including sequence type 10 and two novel sequence types (newly registered as sequence type 172 and sequence type 173). The most prevalent type, sequence type 172 (31/50, 62.0%), had allelic profile 4, 3, 2, 3, 5, 7, 4. In addition, sequence type 10 with allelic profile 4, 3, 2, 3, 5, 3, 4 had a mid-range prevalence (11/50, 22.0%), whereas sequence type 173 with allelic profile 10, 3, 6, 13, 21, 6, 10 was the least prevalent (8/50, 16.0%). Both sequence type 10 and sequence type 172 were clustered in Clonal Complex 3, with isolates from the USA. M. bovis isolates in this study uniformly had low level minimum inhibitory concentrations to enrofloxacin and tiamulin. Overall variances among isolates were significant (Kruskal-Wallis test) for clindamycin (P = 0.006), erythromycin (P = 0.012) and tylosin (P =0.004). Relative to the sequence type 10 group, there were higher minimum inhibitory concentrations levels for the sequence type 173 group (H = -19.795, P = 0.003, for clindamycin; H = -19.574, P = 0.003, for erythromycin; and H = -18.881, P = 0.003, for tylosin) by post-hoc comparisons using pairwise comparisons of mean ranks following Kruskal-Wallis test with Bonferroni correction. Hence, increasing antimicrobial resistance may have contributed to emergence of novel sequence types. These data provided a baseline for elucidating genetic diversity and antibiotic susceptibility profiles of M. bovis in the main dairy-farming provinces in China.

Alternaria Leaf Spot Caused by Alternaria Species: An Emerging Problem on Ornamental Plants in Italy

Serious outbreaks of Alternaria leaf spot and plant decay have recently been recorded on several ornamental plants in the Biella Province (Northern Italy). Twenty-two fungal isolates were obtained from Alternaria infected plant tissues from 13 ornamental hosts. All the isolates were identified morphologically as small-spored Alternaria species. Multilocus sequence typing, carried out by means of ITS, rpb2, tef1, endoPG, Alt a 1, and OPA10-2, assigned 19 isolates as Alternaria alternata, two isolates as belonging to the Alternaria arborescens species complex, and one isolate as an unknown Alternaria sp. Haplotype analyses of ornamental and reference A. alternata isolates from 12 countries identified 14 OPA10-2 and 11 endoPG haplotypes showing a relatively high haplotype diversity. A lack of host specialization or geographic distribution was observed. The host range of the studied A. alternata isolates expanded in cross-pathogenicity assays, and more aggressiveness was frequently observed on the experimental plants than on the host plants from which the fungal isolates were originally isolated. High disease severity, population expansion, intraspecies diversity, and increased range of experimental hosts were seen in the emergence of Alternaria disease on ornamentals. More epidemiological and molecular studies should be performed to better understand these diseases, taking into consideration factors such as seed transmission and ongoing climate changes.

Utilization of Clustered Regularly Interspaced Short Palindromic Repeats to Genotype Escherichia coli Serogroup O80

The hypervariable nature of clustered regularly interspaced short palindromic repeats (CRISPRs) makes them valuable biomarkers for subtyping and epidemiological investigation of Escherichia coli. Shiga toxin-producing E. coli (STEC) serogroup O80 is one hybrid pathotype that is emerging recently in Europe and is involved in hemolytic uremic syndrome with bacteremia. However, whether STEC O80 strains can be genotyped using CRISPR has not been evaluated. In this study, we aimed to characterize the genetic diversity of 81 E. coli serogroup O80 isolates deposited in the National Center for Biotechnology Information databases using CRISPR typing and to explore the association between virulence potential and CRISPR types (CTs). A total of 21 CTs were identified in 80 O80 strains. CRISRP typing provided discrimination with variants of a single serotype, which suggested a stronger discriminatory power. Based on CRISPR spacer profiles, 70 O80:H2 isolates were further divided into four lineages (lineage LI, LII, LIII, and LIV), which correlated well with whole-genome single nucleotide polymorphisms typing and virulence gene profiles. Moreover, the association between CRISPR lineages and virulence gene profiles hinted that STEC O80:H2 strains may originate from O80:H19 or O80:H26 and that lineage LI may have been evolved from lineage LII. CT2 and CT13 were shared by human and cattle isolates, suggesting that there might be the potential transmission between cattle and human. Collectively, CRISPR typing is one technology that can be used to monitor the transmission of STEC O80 strains and provide new insights into microevolution of serogroup O80.

Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes

The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.

Identification of Serogroups Australis and Icterohaemorrhagiae in Two Dogs with a Severe Form of Acute Leptospirosis in Italy

Leptospirosis is an infectious disease that causes serious illness in dogs. For this reason, epidemiological and clinical studies focusing on disease characterization are widely advocated. The aim of this study was to characterize the leptospires identified in dogs with confirmed symptomatic acute leptospirosis. Leptospira spp. DNA detected in urine, blood, or both samples from nine infected dogs was analyzed using the multi-locus sequence typing (MLST) technique. Leptospires from two dogs were successfully typed: one was identified as belonging to Sequence Type (ST) 17 and one to ST198, both within the L. interrogans species, serogroups Icterohaemorrhagiae and Australis, respectively. Based on the results of routine serologic tests, antibodies reactive toward these serogroups are commonly revealed in dogs in Italy. This study provides the first molecular analysis that identifies infecting Leptospira directly on DNA from biological samples of dogs, showing that serogroup Australis can lead to a severe clinical presentation of leptospirosis in infected dogs.

Heterogeneity, Characteristics, and Public Health Implications of Listeria monocytogenes in Ready-to-Eat Foods and Pasteurized Milk in China

Listeria monocytogenes is a foodborne pathogen with a high mortality rate in humans. This study aimed to identify the pathogenic potential of L. monocytogenes isolated from ready-to-eat (RTE) foods and pasteurized milk in China on the basis of its phenotypic and genotypic characteristics. Approximately 7.7% (44/570) samples tested positive for L. monocytogenes among 10.8% (39/360) RTE and 2.4% (5/210) pasteurized milk samples, of which 77.3% (34/44) had < 10 MPN/g, 18.2% (8/44) had 10-110 MPN/g, and 4.5% (2/44) had > 110 MPN/g. A total of 48 strains (43 from RTE foods and five from milk samples) of L. monocytogenes were isolated from 44 positive samples. PCR-serogroup analysis revealed that the most prevalent serogroup was II.2 (1/2b-3b-7), accounting for 52.1% (25/48) of the total, followed by serogroup I.1 (1/2a-3a) accounting for 33.3% (16/48), serogroup I.2 (1/2c-3c) accounting for 12.5% (6/48), and serogroup II.1 (4b-4d-4e) accounting for 2.1%. All isolates were grouped into 11 sequence types (STs) belonging to 10 clonal complexes (CCs) and one singleton (ST619) via multi-locus sequence typing. The most prevalent ST was ST87 (29.2%), followed by ST8 (22.9%), and ST9 (12.5%). Virulence genes determination showed that all isolates harbored eight virulence genes belonging to Listeria pathogenicity islands 1 (LIPI-1) (prfA, actA, hly, mpl, plcA, plcB, and iap) and inlB. Approximately 85.4% isolates carried full-length inlA, whereas seven isolates had premature stop codons in inlA, six of which belonged to ST9 and one to ST5. Furthermore, LLS (encoded by llsX gene, representing LIPI-3) displays bactericidal activity and modifies the host microbiota during infection. LIPI-4 enhances neural and placental tropisms of L. monocytogenes. Results showed that six (12.5%) isolates harbored the llsX gene, and they belonged to ST1/CC1, ST3/CC3, and ST619. Approximately 31.3% (15/48) isolates (belonging to ST87/CC87 and ST619) harbored ptsA (representing LIPI-4), indicating the potential risk of this pathogen. Antimicrobial susceptibility tests revealed that > 95% isolates were susceptible to 16 antimicrobials; however, 60.4 and 22.9% isolates were intermediately resistant to streptomycin and ciprofloxacin, respectively. The results show that several isolates harbor LIPI-3 and LIPI-4 genes, which may be a possible transmission route for Listeria infections in consumers.

State-Wide Genomic and Epidemiological Analyses of Vancomycin-Resistant Enterococcus faecium in Tasmania's Public Hospitals

From 2015 onwards, the number of vancomycin-resistant Enterococcus faecium (VREfm) isolates increased in Tasmania. Previously, we examined the transmission of VREfm at the Royal Hobart Hospital (RHH). In this study, we performed a state-wide analysis of VREfm from Tasmania's four public acute hospitals. Whole-genome analysis was performed on 331 isolates collected from screening and clinical specimens of VREfm. In silico multi-locus sequence typing (MLST) was used to determine the relative abundance of broad sequence types (ST) across the state. Core genome MLST (cgMLST) was then applied to identify potential clades within the ST groupings followed by single-nucleotide polymorphic (SNP) analysis. This work revealed that differences in VREfm profiles are evident between the state's two largest hospitals with the dominant vanA types being ST80 at the RHH and ST1421 at Launceston General Hospital (LGH). A higher number of VREfm cases were recorded at LGH (n = 54 clinical, n = 122 colonization) compared to the RHH (n = 14 clinical, n = 67 colonization) during the same time period, 2014-2016. Eleven of the clinical isolates from LGH were vanA and belonged to ST1421 (n = 8), ST1489 (n = 1), ST233 (n = 1), and ST80 (n = 1) whereas none of the clinical isolates from the RHH were vanA. For the recently described ST1421, cgMLST established the presence of individual clusters within this sequence type that were common to more than one hospital and that included isolates with a low amount of SNP variance (≤16 SNPs). A spatio-temporal analysis revealed that VREfm vanA ST1421 was first detected at the RHH in 2014 and an isolate belonging to the same cgMLST cluster was later collected at LGH in 2016. Inclusion of isolates from two smaller hospitals, the North West Regional Hospital (NRH) and the Mersey Community Hospital (MCH) found that ST1421 was present in both of these institutions in 2017. These findings illustrate the spread of a recently described sequence type of VREfm, ST1421, to multiple hospitals in an Australian state within a relatively short time span.

Isolation and characterization of Salmonella in pork samples collected from retail and wholesale markets in each season from 2016 to 2018 in Wuhan, China

AIMS

To investigate the prevalence and characteristics of Salmonella in pork on sale in Wuhan, Central China.

METHODS AND RESULTS

A total of 4744 pork samples were collected from retail or wholesale markets in each season from 2016 to 2018. The samples showed an overall Salmonella prevalence of 19·54% (927/4744), among which the samples collected in 2017 (21·67%, 428/1975) possessed a significantly higher prevalence than those collected in 2016 (18·61%, 209/1123) (P = 0·047) or 2018 (17·51%, 290/1656) (P = 0·002), and the samples collected in winter showed the lowest prevalence (15·86%, 177/1116). The Salmonella prevalence was significantly higher among samples from retail markets (25·68%, 283/1102) than wholesale markets (17·68%, 644/3642) (P = 0·000). Antimicrobial resistance of 922 Salmonella strains was tested by determining the minimal inhibitory concentrations using a broth microdilution method. The strains revealed that 98·92% (912/922) were resistant to at least one of the antimicrobial agents, and 80·04% (738/922) were resistant to three or more antimicrobials (MDR). Resistance to sulfamethoxazole/trimethoprim (89·91%), tetracycline (87·20%) and ampicillin (71·69%) was predominant. The proportion of MDR strains in 2017 (93·62%, 396/423) was significantly higher than that in 2016 (63·16%, 132/209) (P = 0·000) or 2018 (69·66%, 202/290) (P = 0·000). No significant difference was observed in the proportions of MDR strains between wholesale markets (76·07%, 213/280) and retail markets (80·53%, 517/642) (P = 0·075). Multi-locus sequence typing for 554 of the isolates revealed 20 different sequence types (STs), among which ST40 (38·27%, 212/554), ST34 (18·41%, 102/554) and ST469 (14·46%, 79/554) were dominant.

CONCLUSIONS

A high risk of Salmonella prevalence and antimicrobial resistance was observed in pork in Wuhan. The risk varies between different sampling years, seasons and market types.

SIGNIFICANCE AND IMPACT OF THE STUDY

Providing baseline data on Salmonella contamination in pork on sale in Central China.

Genetic diversity of pathogenic leptospires from wild, domestic and captive host species in Portugal

Leptospirosis is a neglected zoonotic disease of worldwide distribution with a significant veterinary and public health impact. It is caused by pathogenic bacteria of the genus Leptospira. The availability of effective tools to accurately identify and type leptospires is of utmost importance for the diagnosis of the disease and for assessing its epidemiology. Several multi-locus sequence typing (MLST) approaches were described for the typing of worldwide isolates of Leptospira but an extensive agreement towards the adoption of a unique consensus scheme for this agent is still lacking. Most genotyped strains originate from Asian and South American countries, with a minority originating from Europe (being most countries represented only by one or a few isolates). The knowledge of the diversity of circulating leptospires is the key to understanding the disease transmission and its zoonotic implications. In this study, we revisited the taxonomy of several isolates of pathogenic Leptospira obtained from domestic, wild and captive animals in Portugal, between 1990 and 2012. A selection of these isolates was genotyped using two previously published MLST schemes. A total of seven distinct sequence types (STs) were detected among the Portuguese isolates with two STs representing L. borgpetersenii (ST149 and ST152), two STs representing L. kirschneri (ST117 and ST100) and three STs representing L. interrogans (ST17, ST24 and ST140). Global widespread (and maybe more virulent) Leptospira genotypes seem to circulate in Portugal, particularly the L. interrogans ST17 isolates which are associated with several outbreaks of leptospirosis among humans and animals in different regions of the world. This study contributes to the enrichment of the global MLST databases with a new set of allele and sequence type information also providing novel data on circulating Leptospira serovars in Portugal.

Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles

The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.

Genotype Distribution of Panton-Valentine Leukocidin (PVL)-Positive Staphylococcus aureus Strains Isolated from Wound-Related Infections: a Three-Year Multi-Center Study in Tehran, Iran

The spread of Panton-Valentine leucocidin (PVL)-carrying S. aureus strains in patients with wound infections in both the community and hospitals is increasing in some areas of Iran. In the present study, we determined the molecular characteristics and distribution of PVL-producing S. aureus strains isolated from wound infections. Genes encoding resistance, toxins, and staphylococcal enterotoxins were analyzed by polymerase chain reaction assays. Genotyping was performed using multi-locus sequence typing. Aminoglycoside resistance genes including ant (4')-Ia (57.4%) and aac (6')-Ie/aph (2″) (45.7%) were the most prevalent genes in isolates. Staphylococcal enterotoxin type A, as the most frequent type, was present in 20.2% of isolates. Strains belonged to seven clonal complexes. The most frequent clonal complex was CC30 (ST30) (29.8%), followed by CC22 (ST22) (21.3%), CC8 (ST8 and ST931) (17%), CC88 (ST88) (10.6%), CC59 (ST59 and ST338) (8.5%), CC1 (ST772 and ST1) (7.5%), and CC15 (ST15) (5.3%). Our findings indicated an increasing trend of CC30, carrying a wide range of resistance and toxin genes, which could present an obstacle in the treatment of patients with wound infections. Further studies are required to investigate the carriage of resistance, the antibiotic susceptibility pattern, and toxins encoding genes in different molecular types.

Cronobacter sakazakii, Cronobacter malonaticus, and Cronobacter dublinensis Genotyping Based on CRISPR Locus Diversity

Cronobacter strains harboring CRISPR-Cas systems are important foodborne pathogens that cause serious neonatal infections. CRISPR typing is a new molecular subtyping method to track the sources of pathogenic bacterial outbreaks and shows a promise in typing Cronobacter, however, this molecular typing procedure using routine PCR method has not been established. Therefore, the purpose of this study was to establish such methodology, 257 isolates of Cronobacter sakazakii, C. malonaticus, and C. dublinensis were used to verify the feasibility of the method. Results showed that 161 C. sakazakii strains could be divided into 129 CRISPR types (CTs), among which CT15 (n = 7) was the most prevalent CT followed by CT6 (n = 4). Further, 65 C. malonaticus strains were divided into 42 CTs and CT23 (n = 8) was the most prevalent followed by CT2, CT3, and CT13 (n = 4). Finally, 31 C. dublinensis strains belonged to 31 CTs. There was also a relationship among CT, sequence type (ST), food types, and serotype. Compared to multi-locus sequence typing (MLST), this new molecular method has greater power to distinguish similar strains and had better accordance with whole genome sequence typing (WGST). More importantly, some lineages were found to harbor conserved ancestral spacers ahead of their divergent specific spacer sequences; this can be exploited to infer the divergent evolution of Cronobacter and provide phylogenetic information reflecting common origins. Compared to WGST, CRISPR typing method is simpler and more affordable, it could be used to identify sources of Cronobacter food-borne outbreaks, from clinical cases to food sources and the production sites.

Prevalence and Genetic Diversity of Cronobacter Species Isolated From Four Infant Formula Production Factories in China

The aim of this study was to investigate the prevalence and genotypic characteristics of Cronobacter isolated from powdered infant formula (PIF) manufacturing facilities and to identify a potential source of contamination. A total of 42 Cronobacter isolates (5%) were detected in 835 environmental samples collected during the surveillance study. These isolates included C. sakazakii (n = 37), C. malonaticus (n = 3), and C. turicensis (n = 2). The isolates were divided into 14 sequence types (STs) by multi-locus sequence typing (MLST) and 21 pulsotypes (PTs) using pulsed-field gel electrophoresis (PFGE). The dominant C. sakazakii sequence types were ST3 (n = 12) and ST21 (n = 10), followed by ST136 (n = 6). The major PTs were PT22 (n = 12) and PT17 (n = 4) based on 100% similarity. Strains isolated from samples collected at the same production facility showed closer phylogenetic relation than those collected from distinct facilities. The result of extensive traceback sampling showed that PIF residues (PIF dust in production areas), fluid beds, drying areas, floors, and soil samples collected adjacent to the production facilities were the primary positive areas for Cronobacter. The present study outlines an effective approach to determine prevalence and genetic diversity of Cronobacter isolates associated with contamination of PIF.

Multi-locus sequence typing as a tool to investigate environmental sources of infection for cryptococcosis in captive birds

A systematic investigation into environmental sources of infection was conducted at an Australian zoological park after cryptococcosis, caused by Cryptococcus gattii VGI, was diagnosed in a red-tailed black cockatoo (Calyptorhynchus banksii) residing in a large aviary with a diverse range of other avian species. A single tree with an extensive hollow was identified as the likely source of infection based on heavy culture of C. gattii VGI, multi-locus sequence typing and phylogenetic analysis of environmental and disease-related isolates. This led to the careful removal of the tree to reduce the risk of future cases of cryptococcosis in this aviary.

Isolation, Potential Virulence, and Population Diversity of Listeria monocytogenes From Meat and Meat Products in China

Listeria monocytogenes is a globally notorious foodborne pathogen. This study aimed to qualitatively and quantitatively detect L. monocytogenes from meat and meat products in China and to establish their virulence profiles and population diversity. From 1212 meat and meat product samples, 362 (29.9%) were positive for L. monocytogenes. Of these positive samples, 90.6% (328/362) had less than 10 MPN/g, 5.5% (20/364) samples had 10-110 MPN/g, and 3.9% (14/362) of the positive samples had over 110 MPN/g. Serogroup analysis showed that the most prevalent serogroup of L. monocytogenes was I.1 (1/2a-3a), which accounted for 45.0% (123/458) of the total, followed by serogroup I.2 (1/2c-3c) that comprised 26.9%, serogroup II.1 (4b-4d-4e) that comprised 4.8%, and serogroup II.2 (1/2b-3b-7) that comprised 23.3%. A total of 458 isolates were grouped into 35 sequence types (STs) that belonged to 25 clonal complexes (CCs) and one singleton (ST619) by multi-locus sequence typing. The most prevalent ST was ST9 (26.9%), followed by ST8 (17.9%), ST87 (15.3%), ST155 (9.4%), and ST121 (7.6%). Thirty-seven isolates harbored the llsX gene (representing LIPI-3), and they belonged to ST1/CC1, ST3/CC3, ST288/CC288, ST323/CC288, ST330/CC288, ST515/CC1, and ST619, among which ST323/CC288, ST330/CC288, and ST515/CC1 were newly reported to carry LIPI-3. Seventy-five isolates carried ptsA, and they belonged to ST87/CC87, ST88/CC88, and ST619, indicating that consumers may be exposed to potential hypervirulent L. monocytogenes. Antibiotics susceptibility tests revealed that over 90% of the isolates were susceptible to 11 antibiotics; however, 40.0% of the isolates exhibited resistance against ampicillin and 11.8% against tetracycline; further, 45.0 and 4.6% were intermediate resistant and resistant to ciprofloxacin, respectively. The rise of antibiotic resistance in L. monocytogenes suggests that stricter regulations should be formulated to restrict the use of antibiotic agents in human listeriosis treatment and livestock breeding.

Ultrasound gel as a source of hospital outbreaks: Indian experience and literature review

Purpose

Hospital outbreaks are observed increasingly worldwide with various organisms from different sources such as contaminated ultrasound gel, intravenous (IV) fluids and IV medications. Among these, ultrasound gel is one of the most commonly reported sources for Burkholderia cepacia complex (Bcc) outbreaks. In this study, we describe our experience on investigation and the management of Bcc bacteraemia outbreak due to contaminated ultrasound gel from a tertiary care centre, South India.

Materials and Methods

Over a 10-day period in October 2016, seven children in our Paediatric intensive care unit (ICU) were found to have bacteraemia with Bcc isolated from their blood culture. Repeated isolation of the same organism with similar antimicrobial susceptibility pattern over a short incubation period from the same location, confirmed the outbreak. An active outbreak investigation, including environmental surveillance, was carried out to find the source and control the outbreak. Isolates were subjected to multi-locus sequence typing (MLST) and global eBURST (goeBURST) analysis.

Results

Environmental surveillance revealed contaminated ultrasound gel as the source of infection. MLST and goeBURST analysis confirmed that the outbreak was caused by a novel sequence type 1362 with the same clonal complex CC517. The outbreak was controlled by stringent infection control measures, withdrawal of contaminated ultrasound gel from regular usage and implementing the practice of using ultrasonogram (USG) probe cover for USG screening and guided procedures.

Conclusion

This report highlights the importance of early identification of an outbreak, prompt response of the ICU and infection control teams, sound environmental and epidemiological surveillance methods to identify the source and stringent infection control measures to control the outbreak. Contaminated ultrasound gel can be a potential source for healthcare-associated infection, which cannot be overlooked.

Molecular characterization and genotyping of methicillin-resistant Staphylococcus aureus in nasal carriage of healthy Iranian children

PURPOSE

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a considerable public health concern in both developed and developing countries due to the rapid spread of this bacterium around the world, also the epidemiology of MRSA has changed, as the isolation of MRSA strains is not limited to health-care settings or patients with predisposing risk factors. Therefore, the objective of this study is to determine the genetic diversity and antibiotic resistance profile of CA-MRSA nasal carriage in Iranian children.

METHODOLOGY

A cross-sectional study was conducted from April 2013 to March 2014. A total of 25 CA-MRSA were isolated from the anterior nares of 410 preschool children with no risk factors. All MRSA isolates were characterized by detection of the Panton-Valentine leukocidin (pvl) and γ-hemolysin genes, staphylococcal cassette chromosome mec (SCCmec) typing and multi-locus sequence typing (MLST).

RESULTS

In 25 CA-MRSA isolates, Pvl and γ-hemolysin genes were detected in one (4%) and 18 (72 %) isolates; respectively. Overall, 92% (23/25) of isolates belonged to SCCmec type IV and 8% (2/25) of them had SCCmec type V profile. Using MLST, the 25 isolates were grouped into six clonal complexes (CC) and eight sequence types (ST) (CC5/ST6, CC22/ST22 and ST217, CC30/ST30 and ST1107, CC78/ST859, CC398/ST291 and CC97/ST405). The ST859/SCCmec IV (11/25, 44%) was the predominant clone among the isolates. ST859-MRSA-IV-pvl-negative (resistant to tetracycline) have successfully adapted to the Iranian preschool children population.

CONCLUSION

Our results suggest that the genomic diversity was observed among the CA-MRSA. In addition, the current study demonstrates that pvl is not a reliable marker for CA-MRSA in our region.

Occurrence, Antibiotic Resistance, and Population Diversity of Listeria monocytogenes Isolated From Fresh Aquatic Products in China

Listeria monocytogenes is an important Gram-positive foodborne pathogen. However, limited information is available on the comprehensive investigation and potential risk of L. monocytogenes in fresh aquatic products, which are popular to consumers in China. This study aimed to determine the occurrence, virulence profiles, and population diversity of L. monocytogenes isolated from aquatic products in China. In total, 846 aquatic product samples were collected between July 2011 and April 2016 from 43 cities in China. Approximately 7.92% (67/846) aquatic product samples were positive for L. monocytogenes, 86.57% positive samples ranged from 0.3 to 10 MPN/g, whereas 5.97% showed over 110 MPN/g by the Most Probable Number method, which included two samples of products intended to be eaten raw. Serogroups I.1 (serotype 1/2a), I.2 (serotype 1/2b), and III (serotype 4c) were the predominant serogroups isolated, whereas serogroup II.1 (serotype 4b) was detected at much lower frequencies. Examination of antibacterial resistance showed that nine antibacterial resistance profiles were exhibited in 72 isolates, a high level susceptibility of 16 tested antibiotics against L. monocytogenes were observed, indicating these common antibacterial agents are still effective for treating L. monocytogenes infection. Multilocus sequence typing revealed that ST299, ST87, and ST8 are predominant in aquatic products, indicating that the rare ST299 (serotype 4c) may have a special ecological niche in aquatic products and associated environments. Except llsX and ptsA, the 72 isolates harbor nine virulence genes (prfA, actA, hly, plcA, plcB, iap, mpl, inlA, and inlB), premature stop codons (PMSCs) in inlA were found in four isolates, three of which belonged to ST9. A novel PMSC was found in 2929-1LM with a nonsense mutation at position 1605 (TGG→TGA). All ST87 isolates harbored the ptsA gene, whereas 8 isolates (11.11%) carried the llsX gene, and mainly belonged to ST1, ST3, ST308, ST323, ST330, and ST619. Taken together, these results first reported potential virulent L. monocytogenes isolates (ST8 and ST87) were predominant in aquatic products which may have implications for public health in China. It is thus necessary to perform continuous surveillance for L. monocytogenes in aquatic products in China.

Bovine vegetative endocarditis caused by Streptococcus suis

A 5-month-old crossbred beef steer died after exhibiting astasia. A postmortem examination revealed verrucous endocarditis and numerous renal hemorrhages. Gram-positive bacteria were identified in the necrotic lesions of the verruca and mitral valve via histopathological analysis. Multifocal necrosis and hemorrhage were detected in the renal cortex. Gram-positive cocci isolated from the verruca were identified via biochemical tests and 16S rRNA gene sequence analysis as Streptococcus suis. Serotyping indicated that the S. suis isolates were untypable, following which these isolates were classified as a new sequence type (ST1000) via multi-locus sequence typing. S. suis is an important pathogen of pigs. However, clinical cases in cattle are rare. This report is intended to provide information that may be useful in the diagnosis of streptococcal disease in cattle.

Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance

Enterococcus faecium, a major cause of hospital-acquired infections, remains problematic because of its propensity to acquire resistance to vancomycin, which currently is considered first-line therapy. Here, we assess the evolution and resistance acquisition dynamics of E. faecium in a clinical context using a series of 132 bloodstream infection isolates from a single hospital. All isolates, of which 49 (37 %) were vancomycin-resistant, underwent whole-genome sequencing. E. faecium was found to be subject to high rates of recombination with little evidence of sequence importation from outside the local E. faecium population. Apart from disrupting phylogenetic reconstruction, recombination was frequent enough to invalidate MLST typing in the identification of clonal expansion and transmission events, suggesting that, where available, whole-genome sequencing should be used in tracing the epidemiology of E. faecium nosocomial infections and establishing routes of transmission. Several forms of the Tn1549-like element–vanB gene cluster, which was exclusively responsible for vancomycin resistance, appeared and spread within the hospital during the study period. Several transposon gains and losses and instances of in situ evolution were inferred and, although usually chromosomal, the resistance element was also observed on a plasmid background. There was qualitative evidence for clonal expansions of both vancomycin-resistant and vancomycin-susceptible E. faecium with evidence of hospital-specific subclonal expansion. Our data are consistent with continuing evolution of this established hospital pathogen and confirm hospital vancomycin-susceptible and vancomycin-resistant E. faecium patient transmission events, underlining the need for careful consideration before modifying current E. faecium infection control strategies.

Assessment of Microbiological Safety of Water in Public Swimming Pools in Guangzhou, China

This study assessed microbiological safety of water from public swimming pools in Guangzhou, China. Water samples from 39 outdoor municipal swimming pools were collected from late June to early September, 2013 and subjected to detection of protozoa (Giardia and Cryptosporidium) and bacteria (Pseudomonas aeruginos, total coliforms, E. coli, E. coli O157, Shigella, and Salmonella). Cryptosporidium and Giardia were both detected in 5 (12.8%) swimming pools. Total coliforms were detected in 4 (10.3%) samples with concentrations ranging from 1.3 to 154.0 MPN/100 mL while E. coli was detected in 4 (10.3%) samples with concentrations ranging from 0.5 to 5.3 MPN/100 mL. P. aeruginosa was detected in 27 (69.2%) samples but E. coli O157, Shigella and Salmonella were not detected. Among these swimming pools, 9 (23%) met the Chinese National Standard of residual chlorine levels and 24 (62%) were tested free of residual chlorine at least once. The multi-locus sequence typing (MLST) analysis showed that all P. aeruginosa isolates belonged to new sequence types (STs) with dominant ST-1764 and ST-D distributed in different locations within the area. Some P. aeruginosa strains were resistant to medically important antibiotics. Results indicate potential public health risks due to the presence of microbiological pathogens in public swimming pools in this area.

Diaporthe diversity and pathogenicity revealed from a broad survey of grapevine diseases in Europe

Species of Diaporthe are considered important plant pathogens, saprobes, and endophytes on a wide range of plant hosts. Several species are well-known on grapevines, either as agents of pre- or post-harvest infections, including Phomopsis cane and leaf spot, cane bleaching, swelling arm and trunk cankers. In this study we explore the occurrence, diversity and pathogenicity of Diaporthe spp. associated with Vitis vinifera in major grape production areas of Europe and Israel, focusing on nurseries and vineyards. Surveys were conducted in Croatia, Czech Republic, France, Hungary, Israel, Italy, Spain and the UK. A total of 175 Diaporthe strains were isolated from asymptomatic and symptomatic shoots, branches and trunks. A multi-locus phylogeny was established based on five genomic loci (ITS, tef1, cal, his3 and tub2), and the morphological characters of the isolates were determined. Preliminary pathogenicity tests were performed on green grapevine shoots with representative isolates. The most commonly isolated species were D. eres and D. ampelina. Four new Diaporthe species described here as D. bohemiae, D. celeris, D. hispaniae and D. hungariae were found associated with affected vines. Pathogenicity tests revealed D. baccae, D. celeris, D. hispaniae and D. hungariae as pathogens of grapevines. No symptoms were caused by D. bohemiae. This study represents the first report of D. ambigua and D. baccae on grapevines in Europe. The present study improves our understanding of the species associated with several disease symptoms on V. vinifera plants, and provides useful information for effective disease management.

MentaLiST - A fast MLST caller for large MLST schemes

MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data, MLST methods have evolved towards larger typing schemes, based on a few hundred genes [core genome MLST (cgMLST)] to a few thousand genes [whole genome MLST (wgMLST)]. Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes. We introduce MentaLiST, a new MLST caller, based on a k-mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST schemes with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.