Prevalence of High-Risk Antibiotic Resistant Acinetobacter baumannii in the Holy Cities of Makkah and Al-Madinah

Background: Acinetobacter baumannii strains resistant to carbapenems are a global public health problem. Objectives: The aim of the present study is to evaluate the prevalence of genetic fingerprints associated with Metallo β-lactamases in A. baumannii in addition to the clonal diversity of A. baumannii in Makkah and Al-Madinah regions of Saudi Arabia, which receive a high number of international visitors. Methods: Multi-antibiotic resistant A. baumannii isolates were investigated. Bacterial isolation was conducted employing a basic bacteriological technique after confirming the ID of isolates. The antimicrobial susceptibility test was carried out using the Vitek 2 compact system. The molecular clonal diversity of the isolates was determined by Pulse Field Gel Electrophoresis (PFGE). Clusters were analyzed with BioNumerics software version 6.5. Dice coefficient was used for calculating the similarities. Results: The results indicated resistance in 82.5% of A. baumannii isolates against the carbapenems. All the isolates were found to be sensitive to colistin, while 5% of isolates were resistant to tigecycline. The screening of carbapenem-resistant A. baumannii isolates showed that the dissemination of imipenem and meropenem resistance was 81 and 84%, respectively, while the majority of the strains were susceptible to tigecycline and colistin. The blaOXA and blaVIM were the most encountered genes in A. baumannii isolates, while ISAba1 was the prominent insertion sequence. The genetic fingerprinting results (PFGE) revealed two types of epidemic clones: monoclonal and polyclonal models of 17 clusters. Conclusion: The current investigation indicates the diversity in genetic fingerprints of carbapenem-resistant A. baumannii in Makkah and Al-Madinah region of Saudi Arabia, and that two types of epidemic clones are present. It has also been demonstrated that such clones create serious infection dissemination to other parts of the world as heavy pilgrimage traffic is received throughout the year in Makkah and Al-Madinah, especially in the Haj season.

Origin and Dissemination of Altered El Tor Vibrio cholerae O1 Causing Cholera in Odisha, India: Two and Half Decade’s View

The origin, spread and molecular epidemiology of altered El Tor Vibrio cholerae O1 strains isolated from cholera outbreaks/surveillance studies between 1995 and 2019 from different district of Odisha were analyzed. The stock cultures of V. cholerae O1 strains from 1995 to 2019 were analyzed through molecular analysis using different PCR assays and pulse field gel electrophoresis (PFGE) analysis. The spread map (month, year and place) was constructed to locate the dissemination of altered El Tor variants of V. cholerae O1 in this region. A total of 13 cholera outbreaks were caused by V. cholerae O1 Ogawa biotype El Tor carrying ctxB1 and ctxB7 genotypes. The ctxB1 alleles of V. cholerae O1 mostly confined to the coastal areas, whereas the ctxB7 genotypes, though originating in the coastal region of Odisha, concentrated more in the tribal areas. The positive correlation between virulence-associated genes (VAGs) was found through Pearson’s correlation model, indicative of a stronger association between the VAGs. The clonal relationship through PFGE between ctxB1 and ctxB7 genotypes of V. cholerae O1 strains exhibited 80% similarity indicating single- or multi-clonal evolution. It is evident from this study that the spread of multidrug-resistant V. cholerae O1-altered El Tor was dominant over the prototype El Tor strains in this region. The origin of altered El Tor variants of V. cholerae O1 occurred in the East Coast of Odisha established that the origin of cholera happened in the Gangetic belts of Bay of Bengal where all new variants of V. cholerae O1 might have originated from the Asian countries.

An outbreak investigation of Burkholderia cepacia infections related with contaminated chlorhexidine mouthwash solution in a tertiary care center in Turkey

Background We report a nosocomial outbreak caused by Burkholderia cepacia that occurred among six patients admitted in the medical and surgical intensive care unit between 04 March 2019 and 02 April 2019 in Istanbul, Turkey. Methods The outbreak investigation was launched on 11 March 2019 five days after the detection of B. cepacia in four different patients. We defined potential reservoirs and started environmental screening. We sampled the liquid solutions used in patient care activities. Pulse-field gel electrophoresis (PFGE) was performed to determine the genetic relatedness of environmental and patient samples. Results Burkholderia cepacia was isolated in tracheal aspiration cultures of six patients. Three out of six patients developed healthcare-associated pneumoniae due to B. cepacia. Environmental cultures in the ICUs revealed B. cepacia growth in 2% chlorhexidine-gluconate mouthwash solution that been used in the colonized patients as well as in samples obtained from the unused products. PFGE revealed the patient and a specific batch of chlorhexidine mouthwash solution samples had a 96% similarity. Conclusion Contamination of medical solutions used in critical patient care could cause outbreaks and should be detected early by infection control teams. Graphic abstract

A genomic snapshot of Salmonella enterica serovar Typhi in Colombia

Little is known about the genetic diversity of Salmonella enterica serovar Typhi (S. Typhi) circulating in Latin America. It has been observed that typhoid fever is still endemic in this part of the world; however, a lack of standardized blood culture surveillance across Latin American makes estimating the true disease burden problematic. The Colombian National Health Service established a surveillance system for tracking bacterial pathogens, including S. Typhi, in 2006. Here, we characterized 77 representative Colombian S. Typhi isolates collected between 1997 and 2018 using pulse field gel electrophoresis (PFGE; the accepted genotyping method in Latin America) and whole genome sequencing (WGS). We found that the main S. Typhi clades circulating in Colombia were clades 2.5 and 3.5. Notably, the sequenced S. Typhi isolates from Colombia were closely related in a global phylogeny. Consequently, these data suggest that these are endemic clades circulating in Colombia. We found that AMR in S. Typhi in Colombia was uncommon, with a small subset of organisms exhibiting mutations associated with reduced susceptibility to fluoroquinolones. This is the first time that S. Typhi isolated from Colombia have been characterized by WGS, and after comparing these data with those generated using PFGE, we conclude that PFGE is unsuitable for tracking S. Typhi clones and mapping transmission. The genetic diversity of pathogens such as S. Typhi is limited in Latin America and should be targeted for future surveillance studies incorporating WGS.

An Outbreak of Carbapenem-Resistant Klebsiella pneumoniae of K57 Capsular Serotype in an Emergency Intensive Care Unit of a Teaching Hospital in China

The emergence of carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) strains has increased the threat posed by K. pneumoniae. Here, we described an outbreak of 32 CR-hvKP isolates from the emergency intensive care unit (EICU) of a teaching hospital in China. Thirty-two CRKp isolates were collected from six patients and their surrounding environment in EICU. Antimicrobial susceptibility testing was performed using VITEK 2 compact system, E-test or the broth microdilution method. All isolates were serotyped, antimicrobial resistance genes and virulence-associated genes were screened using PCR. Multilocus sequence typing (MLST) and pulse-field gel electrophoresis (PFGE) were employed to characterize the genetic relationships among the CPKP isolates. The virulence capability of 11 CRKp isolates from six patients was evaluated through Galleria mellonella larva infection assay. PFGE showed that all 32 isolates belonged to one cluster, and MLST revealed that belonged to ST11. All isolates exhibited high resistance to β-lactam antibiotics, quinolones, and aminoglycosides. They were susceptible to ceftazidime/averbatan, tigecycline, and colistin. All 32 isolates harbored blaKPC−2, blaSHV−11, blaTEM−1, rmtB, and qnrD. The serotype of all 32 isolates was K57. All 32 isolates contained 6 virulence genes, namely, fimH, iucB, mrkD, rmpA, uge, and wabG. Infection assays demonstrated high mortality in the Galleria mellonella model. Following measures implemented by the hospital, the outbreak was controlled. The mortality rate was 50.0%. The epidemiology of CR-hvKP should be monitored closely to detect early indications of this emerging public health threat.

Helicobacter cinaedi bacteraemia secondary to enterocolitis in an immunocompetent patient

Background Helicobacter cinaedi are motile, gram-negative spiral rods with a natural reservoir in the intestinal tract of hamsters and rhesus monkeys. In humans, H. cinaedi has been reported in different human infections like fever, abdominal pain, gastroenteritis, proctitis, diarrhoea, erysipelas, cellulitis, arthritis, and neonatal meningitis typically diagnosed by positive blood cultures. Even though H. cinaedi has been detected from human blood and stool the entry of H. cinaedi into the blood stream was undocumented until quite recently. The use of pulse-field gel electrophoresis (PFGE) demonstrated that stool- and blood-derived H. cinaedi strains were consistent. Case presentation Here, we describe a rare Danish case of H. cinaedi bacteraemia in an immunocompetent 44-year-old male with diarrhoea. We isolated H. cinaedi from a blood culture taken at admission, and from a FecalSwab taken at day six despite ongoing antibiotic therapy. Next, we made a genetic comparison of both isolates by use of Multi-locus sequence typing (MLST)- and Single nucleotide polymorphism (SNP)-analysis. The two isolates were identical with zero SNPs and by use of MLST the isolate was identified as a novel ST20, confirming previous data of the intestinal tract as a route of H. cinaedi bacteraemia. The results of our AST showed a resistance pattern with higher MICs for ciprofloxacin and clarithromycin than for ampicillin, amoxicillin, gentamicin, and imipenem. The patient was cured with targeted therapy with pivampicillin; however, the primary source of transmission was unknown. Conclusions In conclusion, this case of H. cinaedi bacteraemia secondary to enterocolitis in an immunocompetent patient provide clear evidence that one route of infection occurs through translocation from the intestinal tract to the bloodstream. Helicobacter cinaedi from blood and faeces were identical with a novel ST20, resistant to ciprofloxacin and clarithromycin however, the patient was cured with oral pivampicillin.

Molecular Epidemiology of Salmonellosis in Florida, USA, 2017–2018

The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serotypes. Rarefaction suggested that the serotype richness did not differ between children under 2 years of age and older children and adults and, there are ~22 well-characterized dominant serotypes. There were distinct differences in dominant serotypes between Florida and the USA as a whole, even though S. Enteritidis and S. Newport were the dominant serotypes in Florida and nationally. S. Javiana, S. Sandiego, and S. IV 50:z4, z23:- occurred more frequently in Florida than nationally. Legacy Multi Locus Sequence Typing (MLST) was of limited use for differentiating clinical Salmonella isolates beyond the serotype level. We utilized core genome MLST (cgMLST) hierarchical clusters (HC) to identify potential outbreaks and compared them to outbreaks detected by Pulse Field Gel Electrophoresis (PFGE) surveillance for five dominant serotypes (Enteritidis, Newport, Javiana, Typhimurium, and Bareilly). Single nucleotide polymorphism (SNP) phylogenetic-analysis of cgMLST HC at allelic distance 5 or less (HC5) corroborated PFGE detected outbreaks and generated well-segregated SNP distance-based clades for all studied serotypes. We propose “combination approach” comprising “HC5 clustering,” as efficient tool to trigger Salmonella outbreak investigations, and “SNP-based analysis,” for higher resolution phylogeny to confirm an outbreak. We also applied this approach to identify case clusters, more distant in time and place than traditional outbreaks but may have been infected from a common source, comparing 176 Florida clinical isolates and 1,341 non-clinical isolates across USA, of most prevalent serotype Enteritidis collected during 2017–2018. Several clusters of closely related isolates (0–4 SNP apart) within HC5 clusters were detected and some included isolates from poultry from different states in the US, spanning time periods over 1 year. Two SNP-clusters within the same HC5 cluster included isolates with the same multidrug-resistant profile from both humans and poultry, supporting the epidemiological link. These clusters likely reflect the vertical transmission of Salmonella clones from higher levels in the breeding pyramid to production flocks.

The Prevalence of Virulence Determinants and Antibiotic Resistance Patterns in Methicillin—Resistant Staphylococcus aureus in a Nursing Home in Poland

Nursing homes (NH) contribute to the regional spread of methicillin-resistant Staphylococcus aureus (MRSA). Moreover, residents are vulnerable to the colonization and subsequent infection of MRSA etiology. We aimed at investigating the molecular and phenotypic characteristics of 21 MRSA collected from the residents and personnel in an NH (Lublin, Poland) during 2018. All MRSA were screened for 20 genes encoding virulence determinants (sea-see, eta, etb, tst, lukS-F-PV, eno, cna, ebpS, fib, bbp, fnbA, fnbB, icaADBC) and for resistance to 18 antimicrobials. To establish the relatedness and clonal complexes of MRSA in NH we applied multiple-locus variable-number tandem-repeat fingerprinting (MLVF), pulse field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing. We identified four sequence types (ST) among two clonal complexes (CC): ST (CC22) known as EMRSA-15 as well as three novel STs—ST6295 (CC8), ST6293 (CC8) and ST6294. All tested MRSA were negative for sec, eta, etb, lukS-F-PV, bbp and ebpS genes. The most prevalent gene encoding toxin was sed (52.4%; n = 11/21), and adhesins were eno and fnbA (100%). Only 9.5% (n = 2/21) of MRSA were classified as multidrug-resistant. The emergence of novel MRSA with a unique virulence and the presence of epidemic clone EMRSA-15 creates challenges for controlling the spread of MRSA in NH.

ESBL-producing Klebsiella pneumoniae in a University hospital: Molecular features, diffusion of epidemic clones and evaluation of cross-transmission

The worldwide spread of Klebsiella pneumoniae producing extended-spectrum β-lactamase (ESBL-Kp) is a significant threat. Specifically, various pandemic clones of ESBL-Kp are involved in hospital outbreaks and caused serious infections. In that context, we assessed the phenotypic and molecular features of a collection of ESBL-Kp isolates in a French university hospital and evaluated the occurrence of potential cross-transmissions. Over a 2-year period (2017–2018), 204 non-duplicate isolates of ESBL-Kp were isolated from clinical (n = 118, 57.8%) or screening (n = 86, 42.2%) sample cultures. These isolates were predominantly resistant to cotrimoxazole (88.8%) and ofloxacin (82.8%) but remained susceptible to imipenem (99.3%) and amikacin (93.8%). CTX-M-15 was the most frequent ESBL identified (83.6%). Multilocus sequence typing and pulse-field gel electrophoresis analysis showed an important genetic variability with 41 sequence types (ST) and 50 pulsotypes identified, and the over representation of the international epidemic clones ST307 and ST405. An epidemiological link attesting probable cross-transmission has been identified for 16 patients clustered in 4 groups during the study period. In conclusion, we showed here the dissemination of pandemic clones of ESBL-Kp in our hospital on a background of clonal diversity.

Potential Effectiveness of Piperacillin/Tazobactam in Treating Pediatric Patients Infected With IMP-Type Carbapenemase-producing Enterobacteriaceae

Background: The resistance rate of carbapenem-resistant Enterobacteriaceae (CRE) is increasing yearly but rarely reported in children. Objectives: This retrospective study analyzed the characteristics of isolated CRE strains in pediatric patients, intending to explore reasonable antimicrobial treatment options. Methods: Some CRE isolates were collected from infected pediatric patients in Liaocheng People’s Hospital from January 2014 to December 2019. The strain identification and antimicrobial susceptibility testing were conducted using Vitek mass spectrometry and the Vitek 2 system, respectively. The carbapenemase genotypes of blaKPC, blaIMP, blaVIM, blaNDM-1, and blaOXA-48 were each detected by polymerase chain reaction and sequencing. The molecular homology analysis of strains was conducted via Pulse-field Gel Electrophoresis (PFGE). The clinical data of CRE-infected pediatric patients were collected from the hospital’s medical data information system. Results: Twenty CRE strains were isolated from 1945 infected pediatric patients with Enterobacteriaceae. All CRE strains showed multiple resistance to commonly used antimicrobials. Twelve strains of imipenemase (IMP)-4 and seven strains of IMP-8 carbapenemase were confirmed. Besides, PFGE revealed that two strains of Escherichia coli and three of Klebsiella pneumoniae had indistinguishable patterns. Sixteen patients were cured, including 10 patients using piperacillin/tazobactam. Conclusions: This study found the major sources of resistance were IMP carbapenemases. Piperacillin/tazobactam is potentially effective for the treatment of CRE infection, despite insensitivity in vitro.