The Changing Face of the Family Enterobacteriaceae (Order: "Enterobacterales"): New Members, Taxonomic Issues, Geographic Expansion, and New Diseases and Disease Syndromes.

The family Enterobacteriaceae has undergone significant morphogenetic changes in its more than 85-year history, particularly during the past 2 decades (2000 to 2020). The development and introduction of new and novel molecular methods coupled with innovative laboratory techniques have led to many advances. We now know that the global range of enterobacteria is much more expansive than previously recognized, as they play important roles in the environment in vegetative processes and through widespread environmental distribution through insect vectors. In humans, many new species have been described, some associated with specific disease processes. Some established species are now observed in new infectious disease settings and syndromes. The results of molecular taxonomic and phylogenetics studies suggest that the current family Enterobacteriaceae should possibly be divided into seven or more separate families. The logarithmic explosion in the number of enterobacterial species described brings into question the relevancy, need, and mechanisms to potentially identify these taxa. This review covers the progression, transformation, and morphogenesis of the family from the seminal Centers for Disease Control and Prevention publication (J. J. Farmer III, B. R. Davis, F. W. Hickman-Brenner, A. McWhorter, et al., J Clin Microbiol 21:46-76, 1985, https://doi.org/10.1128/JCM.21.1.46-76.1985) to the present.

Plesiomonas shigelloides Revisited.

After many years in the family Vibrionaceae, the genus Plesiomonas, represented by a single species, P. shigelloides, currently resides in the family Enterobacteriaceae, although its most appropriate phylogenetic position may yet to be determined. Common environmental reservoirs for plesiomonads include freshwater ecosystems and estuaries and inhabitants of these aquatic environs. Long suspected as being an etiologic agent of bacterial gastroenteritis, convincing evidence supporting this conclusion has accumulated over the past 2 decades in the form of a series of foodborne outbreaks solely or partially attributable to P. shigelloides. The prevalence of P. shigelloides enteritis varies considerably, with higher rates reported from Southeast Asia and Africa and lower numbers from North America and Europe. Reasons for these differences may include hygiene conditions, dietary habits, regional occupations, or other unknown factors. Other human illnesses caused by P. shigelloides include septicemia and central nervous system disease, eye infections, and a variety of miscellaneous ailments. For years, recognizable virulence factors potentially associated with P. shigelloides pathogenicity were lacking; however, several good candidates now have been reported, including a cytotoxic hemolysin, iron acquisition systems, and lipopolysaccharide. While P. shigelloides is easy to identify biochemically, it is often overlooked in stool samples due to its smaller colony size or relatively low prevalence in gastrointestinal samples. However, one FDA-approved PCR-based culture-independent diagnostic test system to detect multiple enteropathogens (FilmArray) includes P. shigelloides on its panel. Plesiomonads produce ß-lactamases but are typically susceptible to many first-line antimicrobial agents, including quinolones and carbapenems.

Using a 2-stage strategy with respondent-driven sampling to recruit a hard-to-reach population for a placebo microbicide gel clinical trial in Nellore, Andhra Pradesh (India).

Traditional recruitment methods for microbicide efficacy trials are labor intensive and may fail to reach high-risk hard-to-reach populations. We report duration of recruitment and lessons learned from a two-stage process to recruit female sex workers (FSWs) into a placebo microbicide trial, and examined characteristics associated with successful recruitment of peers who screened for and enrolled in the trial. FSWs were first recruited via respondent-driven sampling (RDS) to complete a survey and subsequently invited to screen for enrollment into a placebo microbicide trial taking place at a local clinic. It took 6 months to enroll 267 participants into the trial. Successful recruiters of peers who enrolled were more likely to have enrolled themselves (AOR 2.0, CI 1.3-2.9) and less likely to visit Nellore city (AOR 0.5, CI 0.3-0.9). Recruitment of FSWs via a two-stage recruitment strategy with RDS can be a good option for future clinical trials.

The genus Shewanella: from the briny depths below to human pathogen.

The genus Shewanella is currently composed of more than 50 species that inhabit a range of marine environs and ecosystems. Several members of this genus, including S. oneidensis, have been identified that could potentially play key roles in environmental processes such as bioremediation of toxic elements and heavy metals and serving as microbial fuel cells. In contrast to this beneficial role, shewanellae are increasingly being implicated as human pathogens in persons exposed through occupational or recreational activities to marine niches containing shewanellae. Documented illnesses linked to Shewanella include skin and soft tissue infections, bacteremia, and otitis media. At present, it is unclear exactly how many Shewanella species are truly bona fide human pathogens. Recent advances in the taxonomy and phylogenetic relatedness of members of this genus, however, support the concept that most human infections are caused by a single species, S. algae. Some phylogenetic data further suggest that some current members of the genus are not true Shewanella species sensu stricto. The current review summarizes our present knowledge of the distribution, epidemiology, disease spectrum, and identification of microbial species focusing on a clinical perspective.

Expedited partner therapy in federally qualified health centers--New York City, 2012.

BACKGROUND: Management of patients' sex partners is a critical element of sexually transmitted disease (STD) control. Expedited partner therapy (EPT), a practice in which patients deliver medication or a prescription directly to their partners, is one option for partner management. As of 2009, New York State law specifically allows EPT for chlamydial infection. Federally qualified health centers (FQHCs) in New York City (NYC) care for patients at risk for STDs. We describe the policies and practices surrounding EPT and other STD management in NYC FQHCs. METHODS: In 2012, we surveyed medical directors at all NYC FQHC parent entities and clinicians at a sample of their corresponding clinical sites about written policies and actual practices regarding EPT for chlamydial infection and other STD management. RESULTS: Twenty-two entities (22/29; 76%) and 51 sites (51/72; 70%) responded to the survey. More than half of entities have a written policy permitting EPT, and 80% of sites provide EPT. Most entity policies allow EPT for, and most sites provide EPT to, adolescents and adults with both opposite-sex and/or same-sex partners. Most sites use electronic health records and provide EPT by prescriptions, and one third of sites do not provide educational materials with EPT. CONCLUSIONS: Our results indicate widespread EPT provision by NYC FQHCs; however, areas for improvement exist, specifically in following guidelines that recommend providing educational materials with EPT and do not recommend EPT for men with male partners. The use of prescriptions for EPT and electronic health records were identified as potential barriers to EPT provision.

Characteristics of female sex workers in southern India willing and unwilling to participate in a placebo gel trial.

Respondent-driven sampling was used to recruit female sex workers (FSWs) for a community survey conducted in southern India. After survey completion, participants were given a brochure describing a clinical trial that entailed daily use of a placebo vaginal gel for four months. This study assessed predictors of screening among survey respondents, predictors of enrollment among those eligible for the trial, and predictors of visit attendance and retention among those enrolled. FSWs who reported having symptoms of sexually transmitted infections (STI), engaging in sex work in the past month, and living in a subdistrict easily accessible by public transportation with a high concentration of FSWs, were more likely to screen. FSWs who had never been tested for HIV were more likely to enroll. This analysis suggests that the primary reason FSWs participated in the trial was a desire for health care-not other factors hypothesized to be important, e.g., HIV risk perception and poverty status.

An evaluation of methods to improve the reporting of adherence in a placebo gel trial in Andhra Pradesh, India.

Female sex workers (FSWs) were recruited for a 4-month placebo vaginal gel trial in Nellore, India. Two experiments explored if prior knowledge of biomarkers for unprotected sex and insertion of gel applicators would yield more accurate self-reports. A third experiment compared self-reports of gel use and adherence levels between FSWs randomly assigned to interactive voice response survey (IVRS) and those assigned to paper diaries. Prior knowledge of biomarkers did not improve accuracy of self-reported condom or gel use, nor did it affect actual adherence. Of those who tested positive for the presence of semenogelin in the vagina, 76% reported no unprotected sex in the previous 48 h. Overall, women reported using gel on 90% of days whereas the biomarker indicated gel use on fewer than 50% of days. Compliance to IVRS was low, despite familiarity with mobile phone technology. Additional explorations with other populations are needed.

Increase in extraintestinal infections caused by Salmonella enterica subspecies II-IV.

To garner information regarding site of infection and age and sex of persons infected with Salmonella enterica subspecies II-IV, we retrospectively analyzed data on Salmonella spp. infections in California, USA, 1985-2009. These subspecies were found to cause significantly more frequent invasive disease (e.g., bacteremia) than did Salmonella subspecies I strains.

Expression of ESBL-like activity in infrequently encountered members of the family Enterobacteriaceae.

A collection of 94 unusual members of the Enterobacteriaceae were screened for the presence of extended spectrum ß-lactamases (ESBLs) using the MicroScan ESßL plus dried confirmation panel. Presumptively positive strains were then confirmed for the presence of an ESBL by double disk diffusion, E-test strips (AB Biodisk, Solna, Sweden) and PCR for SHV, TEM, and CTX-M2 genes. Of the 18 strains initially positive on the ESßL panel only three strains (Leminorella grimontii, Klebsiella ozaenae, and Kluyvera ascorbata) were positive by confirmation methods. These results suggest laboratories should be cautious regarding the methodology employed in screening for the presence of ESBLs in enteric bacteria. However, it should be noted that of the 94 strains, 29 were found to be resistant to two or more of the antibiotics present in the MicroScan ESßL plus panel indicating that there are potential treatment issues with these organisms despite their lack of ESBLs.

The genus Aeromonas: taxonomy, pathogenicity, and infection.

Over the past decade, the genus Aeromonas has undergone a number of significant changes of practical importance to clinical microbiologists and scientists alike. In parallel with the molecular revolution in microbiology, several new species have been identified on a phylogenetic basis, and the genome of the type species, A. hydrophila ATCC 7966, has been sequenced. In addition to established disease associations, Aeromonas has been shown to be a significant cause of infections associated with natural disasters (hurricanes, tsunamis, and earthquakes) and has been linked to emerging or new illnesses, including near-drowning events, prostatitis, and hemolytic-uremic syndrome. Despite these achievements, issues still remain regarding the role that Aeromonas plays in bacterial gastroenteritis, the extent to which species identification should be attempted in the clinical laboratory, and laboratory reporting of test results from contaminated body sites containing aeromonads. This article provides an extensive review of these topics, in addition to others, such as taxonomic issues, microbial pathogenicity, and antimicrobial resistance markers.

Clinical and laboratory diagnostic characteristics and cytotoxigenic potential of Hafnia alvei and Hafnia paralvei strains.

A collection of 68 Hafnia strains previously identified to the species level by 16S rRNA gene sequencing were investigated for simple phenotypic properties that could aid in their recognition in the clinical laboratory. Four tests, including malonate utilization, fermentation of salicin and d-arabinose, and expression of ß-glucosidase activity, correctly assigned each strain to either Hafnia alvei or H. paralvei. Antibiotic susceptibility profiles were generated for 35 H. alvei and H. paralvei isolates using Etest strips for 24 antibiotics. All strains were susceptible to aminoglycosides, quinolones, carbapenems, and monobactams. Most of the Hafnia isolates had a colistin MIC of ≥2 µg/ml. Sequencing of an internal ampC gene fragment allowed genotypic differentiation of the two Hafnia species. Approximately 70% of the hafniae tested additionally produced a cytolytic toxin active on Vero cells which may play a role in gastroenteritis.

Assessing the reporting of adherence and sexual activity in a simulated microbicide trial in South Africa: an interview mode experiment using a placebo gel.

Misreporting of adherence undermines detection of an association between product use and HIV infection in microbicide trials. This study investigates whether, in a placebo trial, audio computer-assisted self-interviewing (ACASI) produces more accurate reporting of adherence and sexual behavior than a face-to-face interview (FTFI). At three South African clinics, 849 women were enrolled and instructed to use applicators filled with placebo gel; participants were randomly assigned to FTFI or ACASI. Behavioral reports were validated through two biomarkers that detect product usage and unprotected sex. For most behaviors, ACASI generated significantly higher reporting, although differences by interview mode appeared to diminish over time. ACASI participants were more likely to report having had sex without gel, but reported and tested applicators did not indicate greater honesty about gel insertion with ACASI. While comparisons of reported unprotected sex with the validated biomarker revealed more agreement with ACASI than with FTFI, differences were small.

The Development of a WTC Environmental Health Center Pan-Cancer Database.

(1) Background: Recent studies have reported elevated risks of multiple cancers in the World Trade Center (WTC) affected community members (also called WTC "Survivors"). The large variety of WTC-cancers created a need to develop a comprehensive cancer database. This paper describes the development of a pan-cancer database at the WTC Environmental Health Center (EHC) Data Center. (2) Methods: A new REDCap-based pan-cancer database was created using the pathology reports and available biomarker data of confirmed cancer cases after review by a cancer epidemiologist, a pathologist, physicians and biostatisticians. (3) Results: The WTC EHC pan-cancer database contains cancer characteristics and emerging biomarker information for cancers of individuals enrolled in the WTC EHC and diagnosed after 11 September 2001 and up to 31 December 2019 obtained from WTC EHC clinical records, pathological reports and state cancer registries. As of 31 December 2019, the database included 3440 cancer cases with cancer characteristics and biomarker information. (4) Conclusions: This evolving database represents an important resource for the scientific community facilitating future research about the etiology, heterogeneity, characteristics and outcomes of cancers and comorbid mental health conditions, cancer economics and gene-environment interaction in the unique population of WTC survivors.

Characteristics of Cancer Patients in the World Trade Center Environmental Health Center.

The destruction of the World Trade Center (WTC) towers on 11 September 2001 released many tons of aerosolized dust and smoke with potential for carcinogenic exposures to community members as well as responders. The WTC Environmental Health Center (WTC EHC) is a surveillance and treatment program for a diverse population of community members ("Survivors"), including local residents and workers, present in the NYC disaster area on 9/11 or in the days or weeks following. We report a case series of cancers identified in the WTC EHC as of 31 December 2019. Descriptive characteristics are presented for 2561 cancer patients (excluding non-melanoma skin cancer) and 5377 non-cancer WTC-EHC participants who signed informed consent. We identified a total of 2999 cancer diagnoses in 2561 patients: 2534 solid tumors (84.5%) and 465 lymphoid and hematopoietic tissue cancers (15.5%) with forty-one different cancer types. We describe the distribution, frequency, median age of cancer diagnosis and median latency from 9/11 by cancer site. In addition to common cancer types, rare cancers, including male breast cancers and mesotheliomas have been identified. The current study is the first report on cancer characteristics of enrollees at WTC EHC, a federally designated treatment and surveillance program for local community members affected by the 9/11 terrorist attack on the WTC.

Evaluation of commercial antisera for Salmonella serotyping.

We compared a set of commercial Salmonella somatic and flagellar serotyping antisera to in-house-prepared antisera from the Microbial Diseases Laboratory, California Department of Public Health, using 327 Salmonella enterica strains belonging to subgroups I, II, IIIa, IIIb, and IV. The sensitivities of Denka Seiken (Tokyo, Japan) somatic and flagellar antisera (using a tube agglutination assay) were 94.0% and 99.2%, respectively, and the specificity was 100% for both sets of sera. Polyvalent O and O1 antiserum sensitivity and specificity were >90%, with the exception of polyvalent O1 antiserum, for which sensitivity was 88.9%. When Denka Seiken flagellar antisera were used in a slide agglutination assay, the sensitivity and accuracy dropped to 88.9% and the specificity fell to 91%. Overall, Denka Seiken commercial antisera performed very well and, together with the comprehensive range of factors available, offer laboratories quality reagents suitable for serotyping strains of salmonellae.

Antioxidant responses to polycyclic aromatic hydrocarbons and organochlorine pesticides in green-lipped mussels (Perna viridis): do mussels "integrate" biomarker responses?

Polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCs) are generally present in the marine environment in complex mixtures. The ecotoxicological nature of contaminant interactions, however, is poorly understood, with most scientific observations derived from single contaminant exposure experiments. The objective of this experiment was to examine dose-response relationships between antioxidant parameters and body contaminant levels in mussels exposed to different exposure regimes under laboratory conditions. Accordingly, the green-lipped mussel, Perna viridis, was challenged with a mixture of PAHs (anthracene, fluoranthene, pyrene, benzo[a]pyrene) and OC pesticides (alpha-HCH, aldrin, dieldrin, p,p'-DDT) over a 4 week period. Contaminants were delivered under four different dosing regimes, with all treatments receiving the same total contaminant load by the end of the exposure period. Antioxidant biomarkers were measured after 1, 2, 3 and 4 weeks, including glutathione (GSH), gluathione-S-transferase (GST), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), glutathione reductase (GR) and lipid peroxidase (LPO). GST and CAT were induced in hepatic tissues in most of the exposure regimes, with the majority of significant induction occurring in a constant exposure regime and a two-step alternate exposure regime. Significant differences among exposure regimes were detected in the body burden of contaminants after 28 days. Hepatic CAT and GSH are proposed as potentially useful biomarkers as they showed good correlation with target contaminants and were not readily affected by different dosing patterns.

A restaurant-associated outbreak of Brainerd diarrhea in California.

In a rare outbreak of Brainerd diarrhea in California, we identified 23 patients, many of whom had diarrhea persisting for > or =6 months. Case-control studies revealed that illness was associated with 1 local restaurant but not with any specific food or beverage. A Campylobacter species was detected in some patients' stool specimens, but its role in the outbreak remains unclear.

Outbreak of Serratia marcescens infections following injection of betamethasone compounded at a community pharmacy.

BACKGROUND: In June 2001, following the report of 4 patients with Serratia marcescens meningitis who received epidural injections of betamethasone compounded at a community pharmacy, we initiated an outbreak investigation. METHODS: All patients who received injections of betamethasone from the production lot common to the 4 patients were evaluated. A case patient was defined as a patient who received compounded betamethasone and had S. marcescens isolated from a sterile site or clinical and laboratory evidence of infection. We cultured all recovered betamethasone, environmental specimens from the pharmacy, and medications recovered from an ambulatory surgery center. The California Board of Pharmacy reviewed the procedures used to prepare the betamethasone. RESULTS: We identified 11 patients with culture-confirmed S. marcescens (8 patients) or clinical infection (3 patients) following injection of compounded betamethasone from 25 May through 31 May 2001. Case patients had meningitis (5 patients, with 3 deaths), epidural abscesses (5 patients), or an infected hip (1 patient). S. marcescens was isolated from 35 (69%) of 51 betamethasone vials recovered, from pharmacy specimens of 1% carboxymethylcellulose stock solution, from pharmacy surfaces, and from multiple parenteral materials used at the ambulatory surgery center. Pulsed-field gel electrophoresis patterns of S. marcescens isolates of representative specimens from patients, the betamethasone, the pharmacy, and the ambulatory surgery center were identical. Deficient practices in compounding of betamethasone included inadequate autoclaving temperatures and failure to perform terminal sterilization. CONCLUSIONS: This outbreak of serious S. marcescens infection followed improper compounding of betamethasone in a community pharmacy. Enforceable national standards for pharmaceutical compounding are needed to reduce the risk of such outbreaks.

Field validation of antioxidant enzyme biomarkers in mussels (Perna viridis) and clams (Ruditapes philippinarum) transplanted in Hong Kong coastal waters.

Green-lipped mussels, Perna viridis, and Manila clams, Ruditapes philippinarum were sourced from "clean" sites in the Hong Kong region, depurated in a laboratory using uncontaminated filtered seawater for 8 days, and transplanted to a suspected gradient of chemically polluted sites in Hong Kong. After 14- and 28-days of field exposure, several antioxidant parameters including glutathione S transferase (GST), catalase (CAT), glutathione peroxidase (GPx), and glutathione (GSH) were quantified in gill and hepatopancreas tissues. Whole body tissue concentrations of polycyclic aromatic hydrocarbons (PAHs), petroleum hydrocarbons (PHCs), polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCs) were determined in pooled site samples. Chemical analyses indicated that: (a) clams had higher levels of PAHs, PHCs, DDTs and PCBs, whereas mussels had higher hexachlorocyclohexane (HCHs) and there was no difference between species for dieldrin and remaining OCs; (b) Kat O should not be continued as a "clean" reference site for Hong Kong, because of the levels of contaminants measured and (c) PAH concentrations in the current survey were similar to those previously measured. Toxicological conclusions were: (a) antioxidant responses were different between species; (b) CAT and GST have highest utility in clams for field use in Hong Kong, whereas CAT in both gill and hepatopancreas tissue showed most potential in mussels; (c) significant induction of antioxidant responses over day 0 (excluding GPx in both tissues, and GST in mussel hepatic tissue); (d) groups of contaminants do not consistently induce antioxidant responses and (e) organochlorines and PCBs correlated significantly with CAT and GST in clam hepatopancreas and with CAT in mussel gill and hepatic tissue. Multivariate statistical techniques indicated little relationship between the site patterns for antioxidant responses and the contaminant gradients identified in body burden analysis.

Uptake and depuration of PAHs and chlorinated pesticides by semi-permeable membrane devices (SPMDs) and green-lipped mussels (Perna viridis).

Semi-batch seawater experiments were conducted to follow the uptake and release of selected PAHs (anthracene, fluorathene, pyrene and B[a]P) and organochlorine pesticides (alpha-HCH, aldrin, dieldrin, p,p'-DDT) in semi-permeable membrane devices (SPMDs) and green-lipped mussels (Perna viridis). Mathematical models were applied to describe the uptake and elimination curves of the contaminants for SPMDs, and kinetic parameters, such as uptake rate constants, and equilibrium triolein/water partitioning coefficients were calculated. SPMD data showed a good fit to estimate rate constant and partition coefficient equations, but only those contaminants which partitioned mainly in the dissolved phase (alpha-HCH and dieldrin) were well explained for mussels. Poor conformity of the other contaminants indicated mussels uptake by routes other than diffusion, such as ingestion of algae. An apparent equilibrium state was only noted for alpha-HCH in mussels. Aldrin was not detected in mussels in the first few days of exposure, indicating potential metabolism of this compound. B[a]P was not detected in the triolein of SPMDs, which suggests that the membrane may act as a reservoir. Loss of spiked B[a]P from the triolein was evident in a depuration experiment, which may indicate transfer to the membrane. Rate constants for mussels were higher than those for SPMDs, but the reverse was true for partition coefficients. Overall, mussels and SPMDs had similar uptake rates for all compounds in this study, excluding p,p'-DDT and dieldrin. Contaminant elimination took place more rapidly in mussels, implying that SPMDs are better candidates for detecting episodic discharge of organic contaminants.